Water micro and bere and lang with gly working with D lang not

diff --git a/PARAM/25_06_23_ions_wat.parm b/PARAM/25_06_23_ions_wat.parm
new file mode 100644 (file)
index 0000000..205eff3
--- /dev/null
+++ b/PARAM/25_06_23_ions_wat.parm
@@ -0,0 +1,176 @@
+2 0 0 0 0 0 0 2 0 0 2 2 2 2 -1 -1 2 1 1 0 0 0 0 0 -1 -1 -1
+1 1 0
+1 1 0
+1 1 0
+1 1 0
+1 1 0
+18 3 0
+1 1 0
+23 3 1
+24 3 2
+39 3 1
+40 3 2
+35.5 3 -1
+65 3 2
+   0.58768   4.70723  -0.56523   0.00000  -0.37777   0.00000   0.00000   0.00000   0.00000   0.00000   2.97950   0.00000   0.00000   0.00000   1.00000   0.00000   0.00000   0.00000   0.00000   0.10164   0.00000   0.00000   0.00000   0.00000   0.00000   0.00000   1.00000   1.00000   1.00000   0.11870   0.10011   0.00000   0.00000   0.00000   0.00000   0.00000   0.00000   1.00000   1.00000   1.00000   0.00000 Cys_Wat 
+   0.48757   4.36438  -0.10008   0.00000  -0.62321   0.00000   0.00000   0.00000   0.00000   0.00000   2.97950   0.00000   0.00000   0.00000   1.00000   0.00000   0.00000   0.00000   0.00000   0.00000   0.00000   0.00000   0.00000   0.00000   0.00000   0.00000   1.00000   1.00000   1.00000   0.00000   0.00000   0.00000   0.00000   0.00000   0.00000   0.00000   0.00000   1.00000   1.00000   1.00000   0.00000 Met_Wat 
+   0.03940   5.02694   0.01422   0.00000  -0.68367   0.00000   0.00000   0.00000   0.00000   0.00000   2.97950   0.00000   0.00000   0.00000   1.00000   0.00000   0.00000   0.00000   0.00000   0.00000   0.00000   0.00000   0.00000   0.00000   0.00000   0.00000   1.00000   1.00000   1.00000   0.00000   0.00000   0.00000   0.00000   0.00000   0.00000   0.00000   0.00000   1.00000   1.00000   1.00000   0.00000 Phe_Wat 
+   0.03466   4.57927   0.03194   0.00000   0.48274   0.00000   0.00000   0.00000   0.00000   0.00000   2.97950   0.00000   0.00000   0.00000   1.00000   0.00000   0.00000   0.00000   0.00000   0.00000   0.00000   0.00000   0.00000   0.00000   0.00000   0.00000   1.00000   1.00000   1.00000   0.00000   0.00000   0.00000   0.00000   0.00000   0.00000   0.00000   0.00000   1.00000   1.00000   1.00000   0.00000 Ile_Wat 
+   0.03466   4.57927   0.03194   0.00000   0.48274   0.00000   0.00000   0.00000   0.00000   0.00000   2.97950   0.00000   0.00000   0.00000   1.00000   0.00000   0.00000   0.00000   0.00000   0.00000   0.00000   0.00000   0.00000   0.00000   0.00000   0.00000   1.00000   1.00000   1.00000   0.00000   0.00000   0.00000   0.00000   0.00000   0.00000   0.00000   0.00000   1.00000   1.00000   1.00000   0.00000 Leu_Wat 
+   0.46647   5.05492  -0.83472   0.00000  -0.84517   0.00000   0.00000   0.00000   0.00000   0.00000   2.97950   0.00000   0.00000   0.00000   1.00000   0.00000   0.00000   0.00000   0.00000   0.00000   0.00000   0.00000   0.00000   0.00000   0.00000   0.00000   1.00000   1.00000   1.00000   0.00000   0.00000   0.00000   0.00000   0.00000   0.00000   0.00000   0.00000   1.00000   1.00000   1.00000   0.00000 Val_Wat 
+   0.03471   5.23211   0.14279   0.00000  -0.46298   0.00000   0.00000   0.00000   0.00000   0.00000   0.29795   0.00000   0.00000   0.00000   1.00000   0.00000   0.00000   0.00000   0.00000   0.00000   0.00000   0.00000   0.00000   0.00000   0.00000   0.00000   1.00000   1.00000   1.00000   0.00000   0.00000   0.00000   0.00000   0.00000   0.00000   0.00000   0.00000   1.00000   1.00000   1.00000   0.00000 Trp_Wat 
+   0.03469   5.80599  -0.39290   0.00000  -0.67892   0.00000   0.00000   0.00000   0.00000   0.00000   2.97950   0.00000   0.00000   0.00000   1.00000   0.00000   0.00000   0.00000   0.00000   0.00000   0.00000   0.00000   0.00000   0.00000   0.00000   0.00000   1.00000   1.00000   1.00000   0.00000   0.00000   0.00000   0.00000   0.00000   0.00000   0.00000   0.00000   1.00000   1.00000   1.00000   0.00000 Tyr_Wat 
+   0.33886   4.80831  -0.70632   0.00000  -0.17959   0.00000   0.00000   0.00000   0.00000   0.00000   2.97950   0.00000   0.00000   0.00000   1.00000   0.00000   0.00000   0.00000   0.00000   0.00000   0.00000   0.00000   0.00000   0.00000   0.00000   0.00000   1.00000   1.00000   1.00000   0.00000   0.00000   0.00000   0.00000   0.00000   0.00000   0.00000   0.00000   1.00000   1.00000   1.00000   0.00000 Ala_Wat 
+   3.09494   2.74193   0.72755   0.00000   0.82658   0.00000   0.00000   0.00000   0.00000   0.00000   0.29795   0.00000   0.00000   0.00000   1.00000   0.00000   0.00000   0.00000   0.00000   0.00000   0.00000   0.00000   0.00000   0.00000   0.00000   0.00000   1.00000   1.00000   1.00000   0.00324   0.11062   0.00000   0.00000   0.00000   0.00000   0.00000   0.00000   1.00000   1.00000   1.00000   0.00000 Gly_Wat 
+   0.42486   4.30589  -0.63453   0.00000  -0.84053   0.00000   0.00000   0.00000   0.00000   0.00000   2.97950   0.00000   0.00000   0.00000   1.00000   0.00000   0.00000   0.00000   0.00000   0.11356   0.00000   0.00000   0.00000   0.00000   0.00000   0.00000   1.00000   1.00000   1.00000   0.22062   0.09877   0.00000   0.00000   0.00000   0.00000   0.00000   0.00000   1.00000   1.00000   1.00000   0.00000 Thr_Wat 
+   2.89301   4.13052  -0.29291   0.00000   0.75500   0.00000   0.00000   0.00000   0.00000   0.00000   2.97950   0.00000   0.00000   0.00000   1.00000   0.00000   0.00000   0.00000   0.00000   0.10017   0.00000   0.00000   0.00000   0.00000   0.00000   0.00000   1.00000   1.00000   1.00000   0.10179   0.10003   0.00000   0.00000   0.00000   0.00000   0.00000   0.00000   1.00000   1.00000   1.00000   0.00000 Ser_Wat 
+   0.05200   3.32602   0.44346   0.00000  -0.08444   0.00000   0.00000   0.00000   0.00000   0.00000   2.97950   0.00000   0.00000   0.00000   1.00000   0.00000   0.00000   0.00000   0.00000   0.10152   0.00000   0.00000   0.00000   0.00000   0.00000   0.00000   1.00000   1.00000   1.00000   0.13018   0.09971   0.00000   0.00000   0.00000   0.00000   0.00000   0.00000   1.00000   1.00000   1.00000   0.00000 Gln_Wat 
+   2.90457   4.19597  -0.27898   0.00000   0.73064   0.00000   0.00000   0.00000   0.00000   0.00000   2.97950   0.00000   0.00000   0.00000   1.00000   0.00000   0.00000   0.00000   0.00000   0.10013   0.00000   0.00000   0.00000   0.00000   0.00000   0.00000   1.00000   1.00000   1.00000   0.10140   0.10002   0.00000   0.00000   0.00000   0.00000   0.00000   0.00000   1.00000   1.00000   1.00000   0.00000 Asn_Wat 
+   0.35034   4.85725  -0.58884   0.00000  -0.12883   0.00000   0.00000   0.00000   0.00000   0.00000   2.97950   0.00000   0.00000   0.00000   1.00000   0.00000   0.00000   0.00000   0.00000   0.00000   0.00000   0.00000   0.00000   0.00000   0.00000   0.00000   1.00000   1.00000   1.00000   0.00331   0.10419   0.00000   0.00000   0.00000   0.00000   0.00000   0.00000   1.00000   1.00000   1.00000   0.00000 Glu_Wat 
+   0.26653   3.95618  -0.50716   0.00000  -0.70774   0.00000   0.00000   0.00000   0.00000   0.00000   2.97950   0.00000   0.00000   0.00000   1.00000   0.00000   0.00000   0.00000   0.00000   0.00000   0.00000   0.00000   0.00000   0.00000   0.00000   0.00000   1.00000   1.00000   1.00000  -0.45179   0.08149   0.00000   0.00000   0.00000   0.00000   0.00000   0.00000   1.00000   1.00000   1.00000   0.00000 Asp_Wat 
+   0.17487   3.34571   0.42472   0.00000  -0.06630   0.00000   0.00000   0.00000   0.00000   0.00000   2.97950   0.00000   0.00000   0.00000   1.00000   0.00000   0.00000   0.00000   0.00000   0.10049   0.00000   0.00000   0.00000   0.00000   0.00000   0.00000   1.00000   1.00000   1.00000   0.11562   0.09976   0.00000   0.00000   0.00000   0.00000   0.00000   0.00000   1.00000   1.00000   1.00000   0.00000 His_Wat 
+   0.03652   3.73385   0.07213   0.00000  -0.27415   0.00000   0.00000   0.00000   0.00000   0.00000   2.97950   0.00000   0.00000   0.00000   1.00000   0.00000   0.00000   0.00000   0.00000   0.00000   0.00000   0.00000   0.00000   0.00000   0.00000   0.00000   1.00000   1.00000   1.00000   0.07695   0.10099   0.00000   0.00000   0.00000   0.00000   0.00000   0.00000   1.00000   1.00000   1.00000   0.00000 Arg_Wat 
+   0.07463   4.77335  -0.21276   0.00000  -0.74350   0.00000   0.00000   0.00000   0.00000   0.00000   2.97950   0.00000   0.00000   0.00000   1.00000   0.00000   0.00000   0.00000   0.00000   0.00000   0.00000   0.00000   0.00000   0.00000   0.00000   0.00000   1.00000   1.00000   1.00000  -0.18116   0.09247   0.00000   0.00000   0.00000   0.00000   0.00000   0.00000   1.00000   1.00000   1.00000   0.00000 Lys_Wat 
+   0.03471   6.34515  -0.70002   0.00000  -0.80060   0.00000   0.00000   0.00000   0.00000   0.00000   2.97950   0.00000   0.00000   0.00000   1.00000   0.00000   0.00000   0.00000   0.00000   0.00000   0.00000   0.00000   0.00000   0.00000   0.00000   0.00000   1.00000   1.00000   1.00000   0.00000   0.00000   0.00000   0.00000   0.00000   0.00000   0.00000   0.00000   1.00000   1.00000   1.00000   0.00000 Pro_Wat 
+   0.48757   4.36438  -0.10008   0.00000  -0.62321   0.00000   0.00000   0.00000   0.00000   0.00000   2.97950   0.00000   0.00000   0.00000   1.00000   0.00000   0.00000   0.00000   0.00000   0.00000   0.00000   0.00000   0.00000   0.00000   0.00000   0.00000   1.00000   1.00000   1.00000   0.00000   0.00000   0.00000   0.00000   0.00000   0.00000   0.00000   0.00000   1.00000   1.00000   1.00000   0.00000 SeMet_Wa
+   0.03940   5.02694   0.01422   0.00000  -0.68367   0.00000   0.00000   0.00000   0.00000   0.00000   2.97950   0.00000   0.00000   0.00000   1.00000   0.00000   0.00000   0.00000   0.00000   0.00000   0.00000   0.00000   0.00000   0.00000   0.00000   0.00000   1.00000   1.00000   1.00000   0.00000   0.00000   0.00000   0.00000   0.00000   0.00000   0.00000   0.00000   1.00000   1.00000   1.00000   0.00000 DapBz_Wa
+   0.33886   4.80831  -0.70632   0.00000  -0.17959   0.00000   0.00000   0.00000   0.00000   0.00000   2.97950   0.00000   0.00000   0.00000   1.00000   0.00000   0.00000   0.00000   0.00000   0.00000   0.00000   0.00000   0.00000   0.00000   0.00000   0.00000   1.00000   1.00000   1.00000   0.00000   0.00000   0.00000   0.00000   0.00000   0.00000   0.00000   0.00000   1.00000   1.00000   1.00000   0.00000 Aib_Wat 
+   0.33886   4.80831  -0.70632   0.00000  -0.17959   0.00000   0.00000   0.00000   0.00000   0.00000   2.97950   0.00000   0.00000   0.00000   1.00000   0.00000   0.00000   0.00000   0.00000   0.00000   0.00000   0.00000   0.00000   0.00000   0.00000   0.00000   1.00000   1.00000   1.00000   0.00000   0.00000   0.00000   0.00000   0.00000   0.00000   0.00000   0.00000   1.00000   1.00000   1.00000   0.00000 Abu_Wat 
+   0.35034   4.85725  -0.58884   0.00000  -0.12883   0.00000   0.00000   0.00000   0.00000   0.00000   2.97950   0.00000   0.00000   0.00000   1.00000   0.00000   0.00000   0.00000   0.00000   0.00000   0.00000   0.00000   0.00000   0.00000   0.00000   0.00000   1.00000   1.00000   1.00000   0.00331   0.10419   0.00000   0.00000   0.00000   0.00000   0.00000   0.00000   1.00000   1.00000   1.00000   0.00000 Glu_Wat 
+   0.35034   4.85725  -0.58884   0.00000  -0.12883   0.00000   0.00000   0.00000   0.00000   0.00000   2.97950   0.00000   0.00000   0.00000   1.00000   0.00000   0.00000   0.00000   0.00000   0.00000   0.00000   0.00000   0.00000   0.00000   0.00000   0.00000   1.00000   1.00000   1.00000   0.00331   0.10419   0.00000   0.00000   0.00000   0.00000   0.00000   0.00000   1.00000   1.00000   1.00000   0.00000 Glu_Wat 
+   0.26653   3.95618  -0.50716   0.00000  -0.70774   0.00000   0.00000   0.00000   0.00000   0.00000   2.97950   0.00000   0.00000   0.00000   1.00000   0.00000   0.00000   0.00000   0.00000   0.00000   0.00000   0.00000   0.00000   0.00000   0.00000   0.00000   1.00000   1.00000   1.00000  -0.45179   0.08149   0.00000   0.00000   0.00000   0.00000   0.00000   0.00000   1.00000   1.00000   1.00000   0.00000 Asp_Wat 
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+3.50339E-01 4.85725E+00 -5.88844E-01 0.00000E+00 -1.28830E-01 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 2.97950E+00 0.00000E+00 0.00000E+00 0.00000E+00 1 0.00 0.00 0.00 0.00 0.00000E+00 0.00000E+00 0.00 0.00 0.00 0.00 0.00 1.0 1.0 1.0 3.31407E-03 1.04186E-01 0.00 0.00 0.00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 1.0 1.0 1.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 Glu_Wat
+2.66525E-01 3.95618E+00 -5.07160E-01 0.00000E+00 -7.07736E-01 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 2.97950E+00 0.00000E+00 0.00000E+00 0.00000E+00 1 0.00 0.00 0.00 0.00 0.00000E+00 0.00000E+00 0.00 0.00 0.00 0.00 0.00 1.0 1.0 1.0 -4.51793E-01 8.14863E-02 0.00 0.00 0.00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 1.0 1.0 1.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 Asp_Wat
+1.74874E-01 3.34571E+00 4.24724E-01 0.00000E+00 -6.62958E-02 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 2.97950E+00 0.00000E+00 0.00000E+00 0.00000E+00 1 0.00 0.00 0.00 0.00 1.00493E-01 0.00000E+00 0.00 0.00 0.00 0.00 0.00 1.0 1.0 1.0 0.00000E+00 0.00000E+00 0.00 0.00 0.00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 1.0 1.0 1.00000E+00 0.00000E+00 1.15621E-01 9.97586E-02 His_Wat
+3.65235E-02 3.73385E+00 7.21323E-02 0.00000E+00 -2.74153E-01 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 2.97950E+00 0.00000E+00 0.00000E+00 0.00000E+00 1 0.00 0.00 0.00 0.00 0.00000E+00 0.00000E+00 0.00 0.00 0.00 0.00 0.00 1.0 1.0 1.0 7.69543E-02 1.00987E-01 0.00 0.00 0.00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 1.0 1.0 1.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 Arg_Wat
+7.46277E-02 4.77335E+00 -2.12759E-01 0.00000E+00 -7.43504E-01 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 2.97950E+00 0.00000E+00 0.00000E+00 0.00000E+00 1 0.00 0.00 0.00 0.00 0.00000E+00 0.00000E+00 0.00 0.00 0.00 0.00 0.00 1.0 1.0 1.0 -1.81159E-01 9.24723E-02 0.00 0.00 0.00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 1.0 1.0 1.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 Lys_Wat
+3.47102E-02 6.34515E+00 -7.00023E-01 0.00000E+00 -8.00596E-01 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 2.97950E+00 0.00000E+00 0.00000E+00 0.00000E+00 1 0.00 0.00 0.00 0.00 0.00000E+00 0.00000E+00 0.00 0.00 0.00 0.00 0.00 1.0 1.0 1.0 0.00000E+00 0.00000E+00 0.00 0.00 0.00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 1.0 1.0 1.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 Pro_Wat
+4.87567E-01 4.36438E+00 -1.00079E-01 0.00000E+00 -6.23208E-01 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 2.97950E+00 0.00000E+00 0.00000E+00 0.00000E+00 1 0.00 0.00 0.00 0.00 0.00000E+00 0.00000E+00 0.00 0.00 0.00 0.00 0.00 1.0 1.0 1.0 0.00000E+00 0.00000E+00 0.00 0.00 0.00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 1.0 1.0 1.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 SeMet_Wat
+3.94000E-02 5.02694E+00 1.42243E-02 0.00000E+00 -6.83672E-01 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 2.97950E+00 0.00000E+00 0.00000E+00 0.00000E+00 1 0.00 0.00 0.00 0.00 0.00000E+00 0.00000E+00 0.00 0.00 0.00 0.00 0.00 1.0 1.0 1.0 0.00000E+00 0.00000E+00 0.00 0.00 0.00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 1.0 1.0 1.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 DapBz_Wat
+3.38861E-01 4.80831E+00 -7.06324E-01 0.00000E+00 -1.79590E-01 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 2.97950E+00 0.00000E+00 0.00000E+00 0.00000E+00 1 0.00 0.00 0.00 0.00 0.00000E+00 0.00000E+00 0.00 0.00 0.00 0.00 0.00 1.0 1.0 1.0 0.00000E+00 0.00000E+00 0.00 0.00 0.00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 1.0 1.0 1.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 Aib_Wat
+3.38861E-01 4.80831E+00 -7.06324E-01 0.00000E+00 -1.79590E-01 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 2.97950E+00 0.00000E+00 0.00000E+00 0.00000E+00 1 0.00 0.00 0.00 0.00 0.00000E+00 0.00000E+00 0.00 0.00 0.00 0.00 0.00 1.0 1.0 1.0 0.00000E+00 0.00000E+00 0.00 0.00 0.00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 1.0 1.0 1.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 Abu_Wat
+3.50339E-01 4.85725E+00 -5.88844E-01 0.00000E+00 -1.28830E-01 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 2.97950E+00 0.00000E+00 0.00000E+00 0.00000E+00 1 0.00 0.00 0.00 0.00 0.00000E+00 0.00000E+00 0.00 0.00 0.00 0.00 0.00 1.0 1.0 1.0 3.31407E-03 1.04186E-01 0.00 0.00 0.00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 1.0 1.0 1.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 Glu_Wat
+3.50339E-01 4.85725E+00 -5.88844E-01 0.00000E+00 -1.28830E-01 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 2.97950E+00 0.00000E+00 0.00000E+00 0.00000E+00 1 0.00 0.00 0.00 0.00 0.00000E+00 0.00000E+00 0.00 0.00 0.00 0.00 0.00 1.0 1.0 1.0 3.31407E-03 1.04186E-01 0.00 0.00 0.00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 1.0 1.0 1.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 Glu_Wat
+2.66525E-01 3.95618E+00 -5.07160E-01 0.00000E+00 -7.07736E-01 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 2.97950E+00 0.00000E+00 0.00000E+00 0.00000E+00 1 0.00 0.00 0.00 0.00 0.00000E+00 0.00000E+00 0.00 0.00 0.00 0.00 0.00 1.0 1.0 1.0 -4.51793E-01 8.14863E-02 0.00 0.00 0.00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 1.0 1.0 1.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 Asp_Wat

diff --git a/source/unres/MD.F90 b/source/unres/MD.F90
index 9fd36be..b0a54b7 100644 (file)
--- a/source/unres/MD.F90
+++ b/source/unres/MD.F90
@@ -699,6 +699,11 @@
        mnum=molnum(i)
         iti=iabs(itype(i,mnum))
         if (mnum.eq.5) iti=itype(i,mnum)
        mnum=molnum(i)
         iti=iabs(itype(i,mnum))
         if (mnum.eq.5) iti=itype(i,mnum)

+!        if (itype(i,mnum).eq.ntyp1_molec(mnum)) then
+!         do j=1,3
+!          incr(j)=d_t(j,i)
+!         enddo
+!        endif

         if (itype(i,1).eq.10 .or. itype(i,mnum).eq.ntyp1_molec(mnum)&
            .or.mnum.ge.3) then
           do j=1,3
         if (itype(i,1).eq.10 .or. itype(i,mnum).eq.ntyp1_molec(mnum)&
            .or.mnum.ge.3) then
           do j=1,3

@@ -726,7 +731,7 @@
          mnum=molnum(i)
          if (itype(i,mnum).ne.ntyp1_molec(mnum)&
          .and.itype(i+1,mnum).ne.ntyp1_molec(mnum)) then
          mnum=molnum(i)
          if (itype(i,mnum).ne.ntyp1_molec(mnum)&
          .and.itype(i+1,mnum).ne.ntyp1_molec(mnum)) then

-         if (mnum.eq.5) Ip(mnum)=Isc(itype(i,mnum),mnum)
+         if (mnum.eq.5) Ip(mnum)=0.0

 !        write (iout,*) "i",i
 !        write (iout,*) "i",i," mag1",mag1," mag2",mag2
          do j=1,3
 !        write (iout,*) "i",i
 !        write (iout,*) "i",i," mag1",mag1," mag2",mag2
          do j=1,3

@@ -922,8 +927,8 @@
 
       do i=innt,inct-1
       mnum=molnum(i)
 
       do i=innt,inct-1
       mnum=molnum(i)

-      if (mnum.eq.5) mp(mnum)=msc(itype(i,mnum),mnum)
-      if (mnum.eq.5) mp(mnum)=msc(itype(i,mnum),mnum)
+      if (mnum.eq.5) mp(mnum)=0.0d0
+!      if (mnum.eq.5) mp(mnum)=msc(itype(i,mnum),mnum)

 !c        write (iout,*) i,(d_t(j,i),j=1,3),(d_t(j,i+1),j=1,3) 
         do j=1,3
           v(j)=0.5d0*(d_t(j,i)+d_t(j,i+1))
 !c        write (iout,*) i,(d_t(j,i),j=1,3),(d_t(j,i+1),j=1,3) 
         do j=1,3
           v(j)=0.5d0*(d_t(j,i)+d_t(j,i+1))

@@ -937,7 +942,11 @@
 !c to the velocities of the first Calpha.
       do i=innt,inct
         mnum=molnum(i)
 !c to the velocities of the first Calpha.
       do i=innt,inct
         mnum=molnum(i)

+        if (mnum.eq.5) then
+        iti=itype(i,mnum)
+        else

         iti=iabs(itype(i,mnum))
         iti=iabs(itype(i,mnum))

+        endif

         if (itype(i,1).eq.10.or.mnum.ge.3.or. itype(i,mnum).eq.ntyp1_molec(mnum)) then
 !c          write (iout,*) i,iti,(d_t(j,i),j=1,3)
           do j=1,3
         if (itype(i,1).eq.10.or.mnum.ge.3.or. itype(i,mnum).eq.ntyp1_molec(mnum)) then
 !c          write (iout,*) i,iti,(d_t(j,i),j=1,3)
           do j=1,3

@@ -961,7 +970,7 @@
          do j=1,3
            incr(j)=d_t(j,i+1)-d_t(j,i)
          enddo
          do j=1,3
            incr(j)=d_t(j,i+1)-d_t(j,i)
          enddo

-         if (mnum.eq.5) Ip(mnum)=Isc(itype(i,mnum),mnum)
+         if (mnum.eq.5) Ip(mnum)=0.0d0

 !c         write (iout,*) i,(incr(j),j=1,3)
 !c         write (iout,*) "Kinetic rotp:",i,(incr(j),j=1,3)
          KEr_p=KEr_p+Ip(mnum)*(incr(1)*incr(1)+incr(2)*incr(2)&
 !c         write (iout,*) i,(incr(j),j=1,3)
 !c         write (iout,*) "Kinetic rotp:",i,(incr(j),j=1,3)
          KEr_p=KEr_p+Ip(mnum)*(incr(1)*incr(1)+incr(2)*incr(2)&

@@ -972,7 +981,13 @@
 !c  The rotational part of the side chain virtual bond
        do i=innt,inct
          mnum=molnum(i)
 !c  The rotational part of the side chain virtual bond
        do i=innt,inct
          mnum=molnum(i)

-         iti=iabs(itype(i,mnum))
+!         iti=iabs(itype(i,mnum))
+        if (mnum.eq.5) then
+        iti=itype(i,mnum)
+        else
+        iti=iabs(itype(i,mnum))
+        endif
+

 !         if (iti.ne.10.and.mnum.lt.3) then
         if (itype(i,1).ne.10.and.mnum.lt.3.and. itype(i,mnum).ne.ntyp1_molec(mnum)) then
            do j=1,3
 !         if (iti.ne.10.and.mnum.lt.3) then
         if (itype(i,1).ne.10.and.mnum.lt.3.and. itype(i,mnum).ne.ntyp1_molec(mnum)) then
            do j=1,3

@@ -1284,8 +1299,11 @@
 
           write (tytul,'("time",f8.2)') totT
           if(mdpdb) then
 
           write (tytul,'("time",f8.2)') totT
           if(mdpdb) then

+             write(iout,*) "before hairpin"

              call hairpin(.true.,nharp,iharp)
              call hairpin(.true.,nharp,iharp)

+             write(iout,*) "before secondary"

              call secondary2(.true.)
              call secondary2(.true.)

+             write(iout,*) "before pdbout"

              call pdbout(potE,tytul,ipdb)
 !             call enerprint(potEcomp)
           else 
              call pdbout(potE,tytul,ipdb)
 !             call enerprint(potEcomp)
           else 

@@ -2272,6 +2290,10 @@
 !      call ginv_mult(fric_work, d_af_work)
 !      call ginv_mult(stochforcvec, d_as_work)
 #ifdef FIVEDIAG
 !      call ginv_mult(fric_work, d_af_work)
 !      call ginv_mult(stochforcvec, d_as_work)
 #ifdef FIVEDIAG

+       write(iout,*) "forces before fivediaginv"
+      do i=1,dimen*3
+       write(iout,*) "fricwork",i,fric_work(i)
+      enddo

       call fivediaginv_mult(dimen,fric_work, d_af_work)
       call fivediaginv_mult(dimen,stochforcvec, d_as_work)
       if (large) then
       call fivediaginv_mult(dimen,fric_work, d_af_work)
       call fivediaginv_mult(dimen,stochforcvec, d_as_work)
       if (large) then

@@ -2382,9 +2404,11 @@
 !      include 'COMMON.INTERACT'
 !      include 'COMMON.IOUNITS'
 !      include 'COMMON.NAMES'
 !      include 'COMMON.INTERACT'
 !      include 'COMMON.IOUNITS'
 !      include 'COMMON.NAMES'

-      real(kind=8),dimension(6*nres) :: stochforcvec,d_as_work1        !(MAXRES6) maxres6=6*maxres
+      real(kind=8),dimension(:),allocatable :: stochforcvec,d_as_work1 !(MAXRES6) maxres6=6*maxres

       real(kind=8) :: cos60 = 0.5d0, sin60 = 0.86602540378443864676d0
       integer :: i,j,ind,inres,mnum
       real(kind=8) :: cos60 = 0.5d0, sin60 = 0.86602540378443864676d0
       integer :: i,j,ind,inres,mnum

+      if (.not.allocated(stochforcvec)) allocate(stochforcvec(6*nres))
+      if (.not.allocated(d_as_work1)) allocate(d_as_work1(6*nres))

 ! Revised 3/31/05 AL: correlation between random contributions to 
 ! position and velocity increments included.
 ! The correlation coefficients are calculated at low-friction limit.
 ! Revised 3/31/05 AL: correlation between random contributions to 
 ! position and velocity increments included.
 ! The correlation coefficients are calculated at low-friction limit.

@@ -3265,7 +3289,7 @@
 !      include 'COMMON.TIME1'
       real(kind=8) :: xv,sigv,lowb,highb  ,Ek1
 #ifdef FIVEDIAG
 !      include 'COMMON.TIME1'
       real(kind=8) :: xv,sigv,lowb,highb  ,Ek1
 #ifdef FIVEDIAG

-      integer ichain,n,innt,inct,ibeg,ierr
+      integer ichain,n,innt,inct,ibeg,ierr,innt_org

       real(kind=8) ,allocatable, dimension(:)::  work
       integer,allocatable,dimension(:) :: iwork
 !      double precision Ghalf(mmaxres2_chain),Geigen(maxres2_chain),&
       real(kind=8) ,allocatable, dimension(:)::  work
       integer,allocatable,dimension(:) :: iwork
 !      double precision Ghalf(mmaxres2_chain),Geigen(maxres2_chain),&

@@ -3311,7 +3335,7 @@
       EK=0.0d0
       Ek3=0.0d0
 #ifdef DEBUG
       EK=0.0d0
       Ek3=0.0d0
 #ifdef DEBUG

-      write(iout,*), nchain
+      write(iout,*), "nchain",nchain

 #endif
       do ichain=1,nchain
         ind=0
 #endif
       do ichain=1,nchain
         ind=0

@@ -3320,7 +3344,9 @@
 !        ghalf=0.0d0
         n=dimen_chain(ichain)
         innt=iposd_chain(ichain)
 !        ghalf=0.0d0
         n=dimen_chain(ichain)
         innt=iposd_chain(ichain)

-        if (molnum(innt).eq.5) go to 137
+!         innt_org=
+        innt_org=chain_border(1,ichain)
+        if ((molnum(innt_org).eq.5).or.(molnum(innt_org).eq.4)) go to 137

         if(.not.allocated(ghalf)) print *,"COCO"
         if(.not.allocated(Ghalf)) allocate(Ghalf(1300*(1300+1)/2))
         ghalf=0.0d0
         if(.not.allocated(ghalf)) print *,"COCO"
         if(.not.allocated(Ghalf)) allocate(Ghalf(1300*(1300+1)/2))
         ghalf=0.0d0

@@ -3394,30 +3420,32 @@
         enddo
 #endif
 137     continue
         enddo
 #endif
 137     continue

-        write(iout,*) "HERE,",n
+        write(iout,*) "HERE,",n,innt
+        innt_org=chain_border(1,ichain)

         xv=0.0d0
         ii=0
         do i=1,n
           do k=1,3
             ii=ii+1
         xv=0.0d0
         ii=0
         do i=1,n
           do k=1,3
             ii=ii+1

-            if (molnum(innt).eq.5) geigen(i)=1.0/msc(itype(innt+i-1,5),5)
-            
+             mnum=molnum(innt_org)
+            if (molnum(innt_org).ge.4) geigen(i)=3.0/msc(itype(innt_org+i-1,mnum),mnum)
+!            if (molnum(innt).eq.5) write(iout,*) "typ",i,innt-1+i,itype(innt+i-1,5)

             sigv=dsqrt((Rb*t_bath)/geigen(i))
             lowb=-5*sigv
             highb=5*sigv
             d_t_work_new(ii)=anorm_distr(xv,sigv,lowb,highb)
             EK=EK+0.5d0*geigen(i)*d_t_work_new(ii)**2
             sigv=dsqrt((Rb*t_bath)/geigen(i))
             lowb=-5*sigv
             highb=5*sigv
             d_t_work_new(ii)=anorm_distr(xv,sigv,lowb,highb)
             EK=EK+0.5d0*geigen(i)*d_t_work_new(ii)**2

-!            write (iout,*) "i",i," ii",ii," geigen",geigen(i), &
-!           " d_t_work_new",d_t_work_new(ii)
+            write (iout,*) "i",i," ii",ii," geigen",geigen(i), &
+           " d_t_work_new",d_t_work_new(ii),innt_org+i-1

           enddo
         enddo
           enddo
         enddo

-        if (molnum(innt).eq.5) then
-    
+        if (molnum(innt_org).ge.4) then
+        mnum=molnum(innt_org)

         do k=1,3
           do i=1,n
             ind=(i-1)*3+k
             d_t_work(ind)=0.0d0
         do k=1,3
           do i=1,n
             ind=(i-1)*3+k
             d_t_work(ind)=0.0d0

-            masinv=1.0/msc(itype(innt+i-1,5),5)
+            masinv=1.0d0/msc(itype(innt_org+i-1,mnum),mnum)

             d_t_work(ind)=d_t_work(ind)&
             +masinv*d_t_work_new((i-1)*3+k)
           enddo
             d_t_work(ind)=d_t_work(ind)&
             +masinv*d_t_work_new((i-1)*3+k)
           enddo

@@ -3503,10 +3531,23 @@
         d_t(:,0)=d_t(:,1)
         d_t(:,1)=0.0d0
       endif
         d_t(:,0)=d_t(:,1)
         d_t(:,1)=0.0d0
       endif

+      if (large) then
+        write (iout,*)
+        write (iout,*) "Random vel after 1st transf the Calpha,SC space"
+        write (iout,'(3hORG,1h(,i5,1h),3f10.5)') 0,(d_t(j,0),j=1,3)
+        do i=1,nres
+          mnum=molnum(i)
+          write (iout,'(a3,1h(,i5,1h),3f10.5,3x,3f10.5)')&
+         restyp(itype(i,mnum),mnum),i,(d_t(j,i),j=1,3),(d_t(j,i+nres),j=1,3)
+        enddo
+      endif
+

 !c      d_a(:,0)=d_a(:,1)
 !c      d_a(:,1)=0.0d0
 !c      write (iout,*) "Shifting accelerations"
       do ichain=2,nchain
 !c      d_a(:,0)=d_a(:,1)
 !c      d_a(:,1)=0.0d0
 !c      write (iout,*) "Shifting accelerations"
       do ichain=2,nchain

+        write(iout,*) "nchain",ichain,chain_border1(1,ichain),molnum(chain_border1(1,ichain))
+        if (molnum(chain_border1(1,ichain)+1).eq.5) cycle

 !c        write (iout,*) "ichain",chain_border1(1,ichain)-1,
 !c     &     chain_border1(1,ichain)
         d_t(:,chain_border1(1,ichain)-1)=d_t(:,chain_border1(1,ichain))
 !c        write (iout,*) "ichain",chain_border1(1,ichain)-1,
 !c     &     chain_border1(1,ichain)
         d_t(:,chain_border1(1,ichain)-1)=d_t(:,chain_border1(1,ichain))

@@ -3514,6 +3555,7 @@
       enddo
 !c      write (iout,*) "Adding accelerations"
       do ichain=2,nchain
       enddo
 !c      write (iout,*) "Adding accelerations"
       do ichain=2,nchain

+        if (molnum(chain_border1(1,ichain)+1).eq.5) cycle

 !c        write (iout,*) "chain",ichain,chain_border1(1,ichain)-1,
 !c     &   chain_border(2,ichain-1)
         d_t(:,chain_border1(1,ichain)-1)=&
 !c        write (iout,*) "chain",ichain,chain_border1(1,ichain)-1,
 !c     &   chain_border(2,ichain-1)
         d_t(:,chain_border1(1,ichain)-1)=&

@@ -3523,10 +3565,23 @@
       do ichain=2,nchain
         write (iout,*) "chain",ichain,chain_border1(1,ichain)-1,&
         chain_border(2,ichain-1)
       do ichain=2,nchain
         write (iout,*) "chain",ichain,chain_border1(1,ichain)-1,&
         chain_border(2,ichain-1)

+        if (molnum(chain_border1(1,ichain)+1).eq.5) cycle
+

         d_t(:,chain_border1(1,ichain)-1)=&
        d_t(:,chain_border1(1,ichain)-1)+d_t(:,chain_border(2,ichain-1))
         d_t(:,chain_border(2,ichain-1))=0.0d0
       enddo
         d_t(:,chain_border1(1,ichain)-1)=&
        d_t(:,chain_border1(1,ichain)-1)+d_t(:,chain_border(2,ichain-1))
         d_t(:,chain_border(2,ichain-1))=0.0d0
       enddo

+      if (large) then
+        write (iout,*)
+        write (iout,*) "Random vel after 2nd transf the Calpha,SC space"
+        write (iout,'(3hORG,1h(,i5,1h),3f10.5)') 0,(d_t(j,0),j=1,3)
+        do i=1,nres
+          mnum=molnum(i)
+          write (iout,'(a3,1h(,i5,1h),3f10.5,3x,3f10.5)')&
+         restyp(itype(i,mnum),mnum),i,(d_t(j,i),j=1,3),(d_t(j,i+nres),j=1,3)
+        enddo
+      endif
+

 #else
       ibeg=0
 !c      do j=1,3
 #else
       ibeg=0
 !c      do j=1,3

@@ -4690,7 +4745,7 @@
         M_PEP=0.0d0
         do i=nnt,nct-1
           mnum=molnum(i)
         M_PEP=0.0d0
         do i=nnt,nct-1
           mnum=molnum(i)

-          if (mnum.ge.5) mp(mnum)=msc(itype(i,mnum),mnum)
+!          if (mnum.ge.5) mp(mnum)=msc(itype(i,mnum),mnum)

           write(iout,*) "WTF",itype(i,mnum),i,mnum,mp(mnum)
 !          if (itype(i,mnum).eq.ntyp1_molec(mnum)) cycle
           M_PEP=M_PEP+mp(mnum)
           write(iout,*) "WTF",itype(i,mnum),i,mnum,mp(mnum)
 !          if (itype(i,mnum).eq.ntyp1_molec(mnum)) cycle
           M_PEP=M_PEP+mp(mnum)

@@ -4705,10 +4760,11 @@
         M_SC=0.0d0                             
         do i=nnt,nct
            mnum=molnum(i)
         M_SC=0.0d0                             
         do i=nnt,nct
            mnum=molnum(i)

-           if (mnum.ge.5) cycle
+!           if (mnum.ge.5) cycle

            iti=iabs(itype(i,mnum))              
           M_SC=M_SC+msc(iabs(iti),mnum)
            inres=i+nres
            iti=iabs(itype(i,mnum))              
           M_SC=M_SC+msc(iabs(iti),mnum)
            inres=i+nres

+           if (mnum.ge.4) inres=i

            do j=1,3
             cm(j)=cm(j)+msc(iabs(iti),mnum)*c(j,inres)     
            enddo
            do j=1,3
             cm(j)=cm(j)+msc(iabs(iti),mnum)*c(j,inres)     
            enddo

@@ -4719,7 +4775,7 @@
 !        write(iout,*) "Center of mass:",cm
         do i=nnt,nct-1
            mnum=molnum(i)
 !        write(iout,*) "Center of mass:",cm
         do i=nnt,nct-1
            mnum=molnum(i)

-          if (mnum.ge.5) mp(mnum)=msc(itype(i,mnum),mnum)
+!          if (mnum.ge.5) mp(mnum)=msc(itype(i,mnum),mnum)

           do j=1,3
             pr(j)=c(j,i)+0.5d0*dc(j,i)-cm(j)
           enddo
           do j=1,3
             pr(j)=c(j,i)+0.5d0*dc(j,i)-cm(j)
           enddo

@@ -4739,8 +4795,9 @@
        do i=nnt,nct    
            mnum=molnum(i)
            iti=iabs(itype(i,mnum))
        do i=nnt,nct    
            mnum=molnum(i)
            iti=iabs(itype(i,mnum))

-           if (mnum.ge.5) cycle
+!          if (mnum.ge.5) cycle

            inres=i+nres
            inres=i+nres

+           if (mnum.ge.4) inres=i

            do j=1,3
              pr(j)=c(j,inres)-cm(j)        
            enddo
            do j=1,3
              pr(j)=c(j,inres)-cm(j)        
            enddo

@@ -5021,7 +5078,7 @@
        summas=0.0d0
        do i=nnt,nct
          mnum=molnum(i)
        summas=0.0d0
        do i=nnt,nct
          mnum=molnum(i)

-         if (mnum.ge.5) mp(mnum)=msc(itype(i,mnum),mnum)
+!         if (mnum.ge.4) mp(mnum)=msc(itype(i,mnum),mnum)

          if (i.lt.nct) then
            summas=summas+mp(mnum)
            do j=1,3
          if (i.lt.nct) then
            summas=summas+mp(mnum)
            do j=1,3

@@ -5029,11 +5086,11 @@
 !             print *,i,j,vv(j),d_t(j,i)
            enddo
          endif
 !             print *,i,j,vv(j),d_t(j,i)
            enddo
          endif

-         if (mnum.ne.4) then 
+!         if (mnum.ne.4) then 

          amas=msc(iabs(itype(i,mnum)),mnum)
          amas=msc(iabs(itype(i,mnum)),mnum)

-         else
-         amas=0.0d0
-         endif
+!         else
+!         amas=0.0d0
+!         endif

          summas=summas+amas                     
          if (itype(i,mnum).ne.10 .and. itype(i,mnum).ne.ntyp1_molec(mnum)&
           .and.(mnum.lt.4)) then
          summas=summas+amas                     
          if (itype(i,mnum).ne.10 .and. itype(i,mnum).ne.ntyp1_molec(mnum)&
           .and.(mnum.lt.4)) then

@@ -5932,6 +5989,7 @@
 !c          innt=chain_border(1,1)
 !c          inct=chain_border(2,1)
           do i=innt,inct
 !c          innt=chain_border(1,1)
 !c          inct=chain_border(2,1)
           do i=innt,inct

+            mnum=molnum(i)

             vvec(ind+1)=v_work(j,i)
             ind=ind+1
 !            if (iabs(itype(i)).ne.10) then
             vvec(ind+1)=v_work(j,i)
             ind=ind+1
 !            if (iabs(itype(i)).ne.10) then

@@ -6152,7 +6210,7 @@
 !      include 'COMMON.IOUNITS'
       integer :: IERROR
       integer :: i,j,ind,ind1,m,ichain,innt,inct
 !      include 'COMMON.IOUNITS'
       integer :: IERROR
       integer :: i,j,ind,ind1,m,ichain,innt,inct

-      logical :: lprn = .false.
+      logical :: lprn = .true.

       real(kind=8) :: dtdi !el ,gamvec(2*nres)
 !el      real(kind=8),dimension(2*nres,2*nres) :: ginvfric,fcopy
 !      real(kind=8),allocatable,dimension(:,:) :: fcopy
       real(kind=8) :: dtdi !el ,gamvec(2*nres)
 !el      real(kind=8),dimension(2*nres,2*nres) :: ginvfric,fcopy
 !      real(kind=8),allocatable,dimension(:,:) :: fcopy

@@ -6261,12 +6319,11 @@
       enddo
 !c DU1fric part
       do ichain=1,nchain
       enddo
 !c DU1fric part
       do ichain=1,nchain

-      mnum=molnum(i)
-

         ind=iposd_chain(ichain)
         innt=chain_border(1,ichain)
         inct=chain_border(2,ichain)
         do i=innt,inct
         ind=iposd_chain(ichain)
         innt=chain_border(1,ichain)
         inct=chain_border(2,ichain)
         do i=innt,inct

+        mnum=molnum(i)

           if (iabs(itype(i,1)).ne.10.and.mnum.le.2) then
             ind=ind+2
           else
           if (iabs(itype(i,1)).ne.10.and.mnum.le.2) then
             ind=ind+2
           else

@@ -6277,11 +6334,11 @@
       enddo
 !c DU2fric part
       do ichain=1,nchain
       enddo
 !c DU2fric part
       do ichain=1,nchain

-      mnum=molnum(i)

         ind=iposd_chain(ichain)
         innt=chain_border(1,ichain)
         inct=chain_border(2,ichain)
         do i=innt,inct-1
         ind=iposd_chain(ichain)
         innt=chain_border(1,ichain)
         inct=chain_border(2,ichain)
         do i=innt,inct-1

+         mnum=molnum(i)

           if (iabs(itype(i,1)).ne.10.and.mnum.le.2) then
             DU2fric(ind)=gamvec(i-nnt+1)/4
             DU2fric(ind+1)=0.0d0
           if (iabs(itype(i,1)).ne.10.and.mnum.le.2) then
             DU2fric(ind)=gamvec(i-nnt+1)/4
             DU2fric(ind+1)=0.0d0

diff --git a/source/unres/REMD.F90 b/source/unres/REMD.F90
index 8649b12..0405dbb 100644 (file)
--- a/source/unres/REMD.F90
+++ b/source/unres/REMD.F90
@@ -49,9 +49,9 @@
 ! the line below might be wrong
 #ifdef FIVEDIAG 
        real(kind=8) :: rs(2*nres),xsolv(2*nres)
 ! the line below might be wrong
 #ifdef FIVEDIAG 
        real(kind=8) :: rs(2*nres),xsolv(2*nres)

-#ifdef CHECK5DSOL
+!#ifdef CHECK5DSOL

        real(kind=8) :: rscheck(2*nres),rsold(2*nres)
        real(kind=8) :: rscheck(2*nres),rsold(2*nres)

-#endif
+!#endif

 #endif
        logical :: lprn = .false.
 !el       common /cipiszcze/ itime
 #endif
        logical :: lprn = .false.
 !el       common /cipiszcze/ itime

@@ -111,11 +111,11 @@
          endif
 #ifdef CHECK5DSOL
 ! Check the solution
          endif
 #ifdef CHECK5DSOL
 ! Check the solution

-          call fivediagmult(n,DMorig(innt),DU1orig(innt),DU2orig(innt),
-     &      xsolv,rscheck)
+          call fivediagmult(n,DMorig(innt),DU1orig(innt),DU2orig(innt),&
+           xsolv,rscheck)

           do i=1,n
           do i=1,n

-            write(iout,*) "i",i,"rsold",rsold(i),"rscheck",rscheck(i),
-     &       "ratio",rscheck(i)/rsold(i)
+            write(iout,*) "i",i,"rsold",rsold(i),"rscheck",rscheck(i),&
+            "ratio",rscheck(i)/rsold(i)

           enddo
 ! end check
 #endif
           enddo
 ! end check
 #endif

@@ -176,6 +176,8 @@
 #define CHUJ
 #ifdef CHUJ
       do ichain=2,nchain
 #define CHUJ
 #ifdef CHUJ
       do ichain=2,nchain

+!TEST 27.06.2023 godz 16.00
+      if (molnum(chain_border1(1,ichain)+1).eq.5) cycle

 !c        write (iout,*) "ichain",chain_border1(1,ichain)-1,
 !c     &     chain_border1(1,ichain)
         d_a(:,chain_border1(1,ichain)-1)=d_a(:,chain_border1(1,ichain))
 !c        write (iout,*) "ichain",chain_border1(1,ichain)-1,
 !c     &     chain_border1(1,ichain)
         d_a(:,chain_border1(1,ichain)-1)=d_a(:,chain_border1(1,ichain))

@@ -183,6 +185,7 @@
       enddo
 !c      write (iout,*) "Adding accelerations"
       do ichain=2,nchain
       enddo
 !c      write (iout,*) "Adding accelerations"
       do ichain=2,nchain

+      if (molnum(chain_border1(1,ichain)+1).eq.5) cycle

 !c        write (iout,*) "chain",ichain,chain_border1(1,ichain)-1,
 !c     &   chain_border(2,ichain-1)
         d_a(:,chain_border1(1,ichain)-1)=&
 !c        write (iout,*) "chain",ichain,chain_border1(1,ichain)-1,
 !c     &   chain_border(2,ichain-1)
         d_a(:,chain_border1(1,ichain)-1)=&

@@ -504,6 +507,7 @@
         mnum=molnum(innt)
         inct=chain_border(2,ichain)
         if (mnum.eq.5) mp(mnum)=0.0
         mnum=molnum(innt)
         inct=chain_border(2,ichain)
         if (mnum.eq.5) mp(mnum)=0.0

+        if (mnum.eq.5) ip(mnum)=0.0

 !        if (mnum.eq.5) mp(mnum)=msc(itype(innt,mnum),mnum)
         DM(ind)=mp(mnum)/4+ip(mnum)/4
         if (iabs(itype(innt,1)).eq.10.or.molnum(innt).gt.2) then
 !        if (mnum.eq.5) mp(mnum)=msc(itype(innt,mnum),mnum)
         DM(ind)=mp(mnum)/4+ip(mnum)/4
         if (iabs(itype(innt,1)).eq.10.or.molnum(innt).gt.2) then

@@ -523,6 +527,7 @@
 !          if (mnum.eq.5) mp(mnum)=msc(itype(i,mnum),mnum)
 !          if (mnum.eq.5) ip(mnum)=isc(itype(i,mnum),mnum)
         if (mnum.eq.5) mp(mnum)=0.0
 !          if (mnum.eq.5) mp(mnum)=msc(itype(i,mnum),mnum)
 !          if (mnum.eq.5) ip(mnum)=isc(itype(i,mnum),mnum)
         if (mnum.eq.5) mp(mnum)=0.0

+        if (mnum.eq.5) ip(mnum)=0.0

 !        if (mnum.eq.5) mp(mnum)=msc(itype(i,mnum),mnum)
           DM(ind)=2*ip(mnum)/4+mp(mnum)/2
           if (iabs(itype(i,1)).eq.10.or.molnum(i).gt.2) then
 !        if (mnum.eq.5) mp(mnum)=msc(itype(i,mnum),mnum)
           DM(ind)=2*ip(mnum)/4+mp(mnum)/2
           if (iabs(itype(i,1)).eq.10.or.molnum(i).gt.2) then

@@ -605,7 +610,8 @@
       enddo
       DMorig=DM
       DU1orig=DU1
       enddo
       DMorig=DM
       DU1orig=DU1

-      DU2orig=DU2
+      DU2orig=DU2     
+      gmatout=.true.

       if (gmatout) then
       write (iout,*)"The upper part of the five-diagonal inertia matrix"
       endif
       if (gmatout) then
       write (iout,*)"The upper part of the five-diagonal inertia matrix"
       endif

@@ -1082,11 +1088,26 @@
       subroutine fivediaginv_mult(ndim,forces,d_a_vec)
       use energy_data, only:nchain,chain_border,nct,nnt,molnum,&
       chain_border1,itype
       subroutine fivediaginv_mult(ndim,forces,d_a_vec)
       use energy_data, only:nchain,chain_border,nct,nnt,molnum,&
       chain_border1,itype

+      use geometry_data, only: nside

       integer ndim
       integer ndim

-      double precision forces(3*ndim),accel(3,0:maxres2),rs(ndim), &
-       xsolv(ndim),d_a_vec(6*nres)
+       
+      real(kind=8),dimension(:),allocatable ::forces,d_a_vec
+      real(kind=8),dimension(:),allocatable :: xsolv,rs
+      real(kind=8),dimension(:,:),allocatable :: accel

       integer i,j,ind,ichain,n,iposc,innt,inct,inct_prev,mnum
       accel=0.0d0
       integer i,j,ind,ichain,n,iposc,innt,inct,inct_prev,mnum
       accel=0.0d0

+!#define DEBUG
+      if (.not.allocated(forces)) allocate(forces(6*nres))
+      if (.not.allocated(d_a_vec)) allocate(d_a_vec(6*nres))
+      if (.not.allocated(xsolv)) allocate(xsolv(3*ndim))
+      if (.not.allocated(rs)) allocate(rs(3*ndim))
+      if (.not.allocated(accel)) allocate(accel(3,0:2*nres))
+
+#ifdef DEBUG
+      do i=1,6*nres
+       write(iout,*) "received forces",i,forces(i)
+      enddo
+#endif

       do j=1,3
 !Compute accelerations in Calpha and SC
         do ichain=1,nchain
       do j=1,3
 !Compute accelerations in Calpha and SC
         do ichain=1,nchain

@@ -1095,12 +1116,16 @@
           innt=chain_border(1,ichain)
           inct=chain_border(2,ichain)
           do i=iposc,iposc+n-1
           innt=chain_border(1,ichain)
           inct=chain_border(2,ichain)
           do i=iposc,iposc+n-1

+!            write(iout,*) "index",3*(i-1)+j,forces(3*(i-1)+j)

             rs(i-iposc+1)=forces(3*(i-1)+j)
           enddo
 #ifdef DEBUG
             rs(i-iposc+1)=forces(3*(i-1)+j)
           enddo
 #ifdef DEBUG

-          write (iout,*) "j",j," chain",ichain
+          write (iout,*) "j",j," chain",ichain,"n",n
+          write (iout,*) "innt",innt,inct,iposc

           write (iout,*) "rs"
           write (iout,*) "rs"

-          write (iout,'(f10.5)') (rs(i),i=1,n)
+          do i=1,n
+          write (iout,'(i5,f10.5)') i,rs(i)
+          enddo

 #endif
           call FDISYS (n,DM(iposc),DU1(iposc),DU2(iposc),rs,xsolv)
 #ifdef DEBUG
 #endif
           call FDISYS (n,DM(iposc),DU1(iposc),DU2(iposc),rs,xsolv)
 #ifdef DEBUG

@@ -1125,8 +1150,8 @@
 #ifdef DEBUG
       write (iout,*) "accel in CA-SC basis"
       do i=1,nres
 #ifdef DEBUG
       write (iout,*) "accel in CA-SC basis"
       do i=1,nres

-        write (iout,'(i5,3f10.5,5x,3f10.5)') i,(accel(j,i),j=1,3),
-     &      (accel(j,i+nres),j=1,3)
+        write (iout,'(i5,3f10.5,5x,3f10.5)') i,(accel(j,i),j=1,3),&
+           (accel(j,i+nres),j=1,3)

       enddo
       write (iout,*) "nnt",nnt
 #endif
       enddo
       write (iout,*) "nnt",nnt
 #endif

@@ -1155,11 +1180,13 @@
         accel(:,1)=0.0d0
       endif
       do ichain=2,nchain
         accel(:,1)=0.0d0
       endif
       do ichain=2,nchain

+      if (molnum(chain_border1(1,ichain)+1).eq.5) cycle

         accel(:,chain_border1(1,ichain)-1)= &
          accel(:,chain_border1(1,ichain))
         accel(:,chain_border1(1,ichain))=0.0d0
       enddo
       do ichain=2,nchain
         accel(:,chain_border1(1,ichain)-1)= &
          accel(:,chain_border1(1,ichain))
         accel(:,chain_border1(1,ichain))=0.0d0
       enddo
       do ichain=2,nchain

+      if (molnum(chain_border1(1,ichain)+1).eq.5) cycle

         accel(:,chain_border1(1,ichain)-1)= &
        accel(:,chain_border1(1,ichain)-1) &
         +accel(:,chain_border(2,ichain-1))
         accel(:,chain_border1(1,ichain)-1)= &
        accel(:,chain_border1(1,ichain)-1) &
         +accel(:,chain_border(2,ichain-1))

@@ -1197,7 +1224,7 @@
 #endif
       return
       end subroutine
 #endif
       return
       end subroutine

-
+#undef DEBUG

 
 #else
 !-----------------------------------------------------------------------------
 
 #else
 !-----------------------------------------------------------------------------

diff --git a/source/unres/compare.F90 b/source/unres/compare.F90
index 6d00c0a..1dfe01e 100644 (file)
--- a/source/unres/compare.F90
+++ b/source/unres/compare.F90
@@ -161,15 +161,16 @@
 !      include 'COMMON.FFIELD'
 !      include 'COMMON.NAMES'
       integer :: ncont
 !      include 'COMMON.FFIELD'
 !      include 'COMMON.NAMES'
       integer :: ncont

-      integer,dimension(2,100*nres) :: icont   !(2,maxcont)    (maxcont=12*maxres)
+      integer,dimension(:,:),allocatable :: icont      !(2,maxcont)    (maxcont=12*maxres)

       integer :: nharp
       integer,dimension(4,nres) :: iharp       !(4,nres/3)(4,maxres/3)
       logical :: lprint,not_done
       real(kind=8) :: rcomp=6.0d0
 !el local variables
       integer :: i,j,kkk,k,i1,i2,it1,it2,j1,ii1,jj1
       integer :: nharp
       integer,dimension(4,nres) :: iharp       !(4,nres/3)(4,maxres/3)
       logical :: lprint,not_done
       real(kind=8) :: rcomp=6.0d0
 !el local variables
       integer :: i,j,kkk,k,i1,i2,it1,it2,j1,ii1,jj1

-!      allocate(icont(2,100*nres))
-
+      if (.not.allocated(icont)) then
+      allocate(icont(2,100*nres_molec(1)+1))
+      endif

       ncont=0
       kkk=0
 !     print *,'nnt=',nnt,' nct=',nct
       ncont=0
       kkk=0
 !     print *,'nnt=',nnt,' nct=',nct

@@ -269,8 +270,8 @@
       real(kind=8) :: ael6_i,ael3_i
       real(kind=8),dimension(2,2) :: app_,bpp_,rpp_
       integer :: ncont
       real(kind=8) :: ael6_i,ael3_i
       real(kind=8),dimension(2,2) :: app_,bpp_,rpp_
       integer :: ncont

-      integer,dimension(2,100*nres) :: icont   !(2,100*nres)(2,maxcont)        (maxcont=12*maxres)
-      real(kind=8),dimension(100*nres) :: econt        !(maxcont)
+      integer,dimension(:,:),allocatable :: icont      !(2,100*nres)(2,maxcont)        (maxcont=12*maxres)
+      real(kind=8),dimension(:),allocatable :: econt   !(maxcont)

 !el local variables
       integer :: i,j,k,iteli,itelj,i1,i2,it1,it2,ic1,ic2
       real(kind=8) :: elcutoff,elecutoff_14,rri,ees,evdw
 !el local variables
       integer :: i,j,k,iteli,itelj,i1,i2,it1,it2,ic1,ic2
       real(kind=8) :: elcutoff,elecutoff_14,rri,ees,evdw

@@ -292,7 +293,12 @@
       data elpp_3  / 0.0503d0, 0.0000d0, 0.0000d0, 0.0692d0/
 
 !el      allocate(econt(100*nres))     !(maxcont)
       data elpp_3  / 0.0503d0, 0.0000d0, 0.0000d0, 0.0692d0/
 
 !el      allocate(econt(100*nres))     !(maxcont)

-
+      if (.not.allocated(icont)) then
+       allocate(icont(2,100*nres_molec(1)+1))
+      endif
+      if (.not.allocated(econt)) then
+       allocate(econt(100*nres_molec(1)+1))
+      endif

       elcutoff = -0.3d0
       elecutoff_14 = -0.5d0
       if (lprint) write (iout,'(a)') &
       elcutoff = -0.3d0
       elecutoff_14 = -0.5d0
       if (lprint) write (iout,'(a)') &

@@ -483,7 +489,7 @@
 !      include 'COMMON.CONTROL'
       integer :: ncont,i,j,i1,j1,nbeta,nstrand,ii1,jj1,ij,nhelix,&
              iii1,jjj1
 !      include 'COMMON.CONTROL'
       integer :: ncont,i,j,i1,j1,nbeta,nstrand,ii1,jj1,ij,nhelix,&
              iii1,jjj1

-      integer,dimension(2,100*nres) :: icont   !(2,maxcont)    (maxcont=12*maxres)
+      integer,dimension(:,:),allocatable :: icont      !(2,maxcont)    (maxcont=12*maxres)

       integer,dimension(nres,0:4) :: isec      !(maxres,4)
       integer,dimension(nres) :: nsec  !(maxres)
       logical :: lprint,not_done       !,freeres
       integer,dimension(nres,0:4) :: isec      !(maxres,4)
       integer,dimension(nres) :: nsec  !(maxres)
       logical :: lprint,not_done       !,freeres

@@ -491,7 +497,9 @@
 !el      external freeres
 
 !el      allocate(icont(2,100*nres),isec(nres,4),nsec(nres))
 !el      external freeres
 
 !el      allocate(icont(2,100*nres),isec(nres,4),nsec(nres))

-
+      if (.not.allocated(icont)) then
+       allocate(icont(2,100*nres+1))
+      endif

       if(.not.dccart) call chainbuild_cart
       if(.not.allocated(hfrag)) allocate(hfrag(2,nres/3)) !(2,maxres/3)
 !d      call write_pdb(99,'sec structure',0d0)
       if(.not.dccart) call chainbuild_cart
       if(.not.allocated(hfrag)) allocate(hfrag(2,nres/3)) !(2,maxres/3)
 !d      call write_pdb(99,'sec structure',0d0)

@@ -2373,9 +2381,9 @@
 !      include 'COMMON.IOUNITS'
 !      include 'COMMON.DISTFIT'
 
 !      include 'COMMON.IOUNITS'
 !      include 'COMMON.DISTFIT'
 

-      integer :: ncont,icont(2,nres*nres/2),isec(nres,3)
+      integer :: ncont,isec(nres,3)

       logical :: lprint,not_done
       logical :: lprint,not_done

-      real(kind=4) :: dcont(nres*nres/2),d
+      real(kind=4) :: d

       real(kind=4) :: rcomp = 7.0
       real(kind=4) :: rbeta = 5.2
       real(kind=4) :: ralfa = 5.2
       real(kind=4) :: rcomp = 7.0
       real(kind=4) :: rbeta = 5.2
       real(kind=4) :: ralfa = 5.2

@@ -2383,6 +2391,14 @@
       real(kind=8),dimension(3) :: xpi,xpj
       integer :: i,k,j,i1,j1,nbeta,nstrand,ii1,jj1,ij,iii1,jjj1,&
             nhelix
       real(kind=8),dimension(3) :: xpi,xpj
       integer :: i,k,j,i1,j1,nbeta,nstrand,ii1,jj1,ij,iii1,jjj1,&
             nhelix

+      integer, dimension(:,:),allocatable :: icont
+      real(kind=4),dimension(:),allocatable :: dcont
+      if (.not.allocated(icont)) then
+        allocate(icont(2,100*nres_molec(1)+1))
+      endif
+      if (.not.allocated(dcont)) then
+       allocate(dcont(100*nres_molec(1)+1))
+      endif

       call chainbuild_cart
 !d      call write_pdb(99,'sec structure',0d0)
       ncont=0
       call chainbuild_cart
 !d      call write_pdb(99,'sec structure',0d0)
       ncont=0

@@ -2410,6 +2426,7 @@
                (xpi(2)-xpj(2))*(xpi(2)-xpj(2)) + &
                (xpi(3)-xpj(3))*(xpi(3)-xpj(3)) 
          if ( d.lt.rcomp*rcomp) then
                (xpi(2)-xpj(2))*(xpi(2)-xpj(2)) + &
                (xpi(3)-xpj(3))*(xpi(3)-xpj(3)) 
          if ( d.lt.rcomp*rcomp) then

+            if (ncont.gt.(100*nres_molec(1)+1)) ncont=100*nres_molec(1)+1

             ncont=ncont+1
             icont(1,ncont)=i
             icont(2,ncont)=j
             ncont=ncont+1
             icont(1,ncont)=i
             icont(2,ncont)=j

diff --git a/source/unres/energy.F90 b/source/unres/energy.F90
index 572dd3e..d4be24e 100644 (file)
--- a/source/unres/energy.F90
+++ b/source/unres/energy.F90
@@ -12731,9 +12731,9 @@ C !!!!!!!! NIE CZYTANE !!!!!!!!!!!
 !       print *,i,j,gg_lipi(3),gg_lipj(3),sss_ele_cut
 !      write (iout,*) "gg",(gg(k),k=1,3)
       do k=1,3
 !       print *,i,j,gg_lipi(3),gg_lipj(3),sss_ele_cut
 !      write (iout,*) "gg",(gg(k),k=1,3)
       do k=1,3

-        gradpepcatx(k,i)=gradpepcatx(k,i)-gg(k) &
+        gradpepcatx(k,i)=gradpepcatx(k,i)-gg(k)*sss_ele_cut &

                   +(eom12*(dc_norm(k,j)-om12*dc_norm(k,nres+i)) &
                   +(eom12*(dc_norm(k,j)-om12*dc_norm(k,nres+i)) &

-                  +eom1*(erij(k)-om1*dc_norm(k,nres+i)))*dsci_inv
+                  +eom1*(erij(k)-om1*dc_norm(k,nres+i)))*dsci_inv*sss_ele_cut

 
 !        gradpepcatx(k,j)=gradpepcatx(k,j)+gg(k) &
 !                  +(eom12*(dc_norm(k,nres+i)-om12*dc_norm(k,j)) &
 
 !        gradpepcatx(k,j)=gradpepcatx(k,j)+gg(k) &
 !                  +(eom12*(dc_norm(k,nres+i)-om12*dc_norm(k,j)) &

@@ -12748,8 +12748,8 @@ C !!!!!!!! NIE CZYTANE !!!!!!!!!!!
 ! Calculate the components of the gradient in DC and X
 !
       do l=1,3
 ! Calculate the components of the gradient in DC and X
 !
       do l=1,3

-        gradpepcat(l,i)=gradpepcat(l,i)-gg(l)
-        gradpepcat(l,j)=gradpepcat(l,j)+gg(l)
+        gradpepcat(l,i)=gradpepcat(l,i)-gg(l)*sss_ele_cut
+        gradpepcat(l,j)=gradpepcat(l,j)+gg(l)*sss_ele_cut

       enddo
       end subroutine sc_grad_cat
 
       enddo
       end subroutine sc_grad_cat
 

@@ -12769,20 +12769,21 @@ C !!!!!!!! NIE CZYTANE !!!!!!!!!!!
 !      eom2=0.0d0
 !      eom12=evdwij*eps1_om12
 ! end diagnostics
 !      eom2=0.0d0
 !      eom12=evdwij*eps1_om12
 ! end diagnostics

+!      write (iout,*) "gg",(gg(k),k=1,3)

 
       do k=1,3
         dcosom1(k) = rij * (dc_norm(k,i) - om1 * erij(k))
         dcosom2(k) = rij * (dc_norm(k,nres+j) - om2 * erij(k))
         gg(k) = gg(k) + eom1 * dcosom1(k) + eom2 * dcosom2(k)
 
       do k=1,3
         dcosom1(k) = rij * (dc_norm(k,i) - om1 * erij(k))
         dcosom2(k) = rij * (dc_norm(k,nres+j) - om2 * erij(k))
         gg(k) = gg(k) + eom1 * dcosom1(k) + eom2 * dcosom2(k)

-        gvdwc_pepbase(k,i)= gvdwc_pepbase(k,i) +0.5*(- gg(k))   &
+        gradpepcat(k,i)= gradpepcat(k,i) +sss_ele_cut*(0.5*(- gg(k))   &

                  + (-eom12*(dc_norm(k,nres+j)-om12*dc_norm(k,i)))&
                  *dsci_inv*2.0 &
                  + (-eom12*(dc_norm(k,nres+j)-om12*dc_norm(k,i)))&
                  *dsci_inv*2.0 &

-                 - (eom1*(erij(k)-om1*dc_norm(k,i)))*dsci_inv*2.0
-        gvdwc_pepbase(k,i+1)= gvdwc_pepbase(k,i+1) +0.5*(- gg(k))   &
+                 - (eom1*(erij(k)-om1*dc_norm(k,i)))*dsci_inv*2.0)
+        gradpepcat(k,i+1)= gradpepcat(k,i+1) +sss_ele_cut*(0.5*(- gg(k))   &

                  - (-eom12*(dc_norm(k,nres+j)-om12*dc_norm(k,i))) &
                  *dsci_inv*2.0 &
                  - (-eom12*(dc_norm(k,nres+j)-om12*dc_norm(k,i))) &
                  *dsci_inv*2.0 &

-                 + (eom1*(erij(k)-om1*dc_norm(k,i)))*dsci_inv*2.0
-        gradpepcat(k,j)=gradpepcat(k,j)+gg(k)
+                 + (eom1*(erij(k)-om1*dc_norm(k,i)))*dsci_inv*2.0)
+        gradpepcat(k,j)=gradpepcat(k,j)+gg(k)*sss_ele_cut

       enddo
       end subroutine sc_grad_cat_pep
 
       enddo
       end subroutine sc_grad_cat_pep
 

@@ -23774,7 +23775,7 @@ C !!!!!!!! NIE CZYTANE !!!!!!!!!!!
       real(kind=8) :: xj_safe,yj_safe,zj_safe,xj_temp,yj_temp,zj_temp,&
                 dist_temp, dist_init,ssgradlipi,ssgradlipj, &
                 sslipi,sslipj,faclip,alpha_sco
       real(kind=8) :: xj_safe,yj_safe,zj_safe,xj_temp,yj_temp,zj_temp,&
                 dist_temp, dist_init,ssgradlipi,ssgradlipj, &
                 sslipi,sslipj,faclip,alpha_sco

-      integer :: ii
+      integer :: ii,ki

       real(kind=8) :: fracinbuf
       real (kind=8) :: escpho
       real (kind=8),dimension(4):: ener
       real(kind=8) :: fracinbuf
       real (kind=8) :: escpho
       real (kind=8),dimension(4):: ener

@@ -23806,7 +23807,10 @@ C !!!!!!!! NIE CZYTANE !!!!!!!!!!!
       enddo
 !        go to 17
 !        do i=1,nres_molec(1)-1  ! loop over all peptide groups needs parralelization
       enddo
 !        go to 17
 !        do i=1,nres_molec(1)-1  ! loop over all peptide groups needs parralelization

-      do i=ibond_start,ibond_end
+!      do i=ibond_start,ibond_end
+      do ki=g_listcatscnorm_start,g_listcatscnorm_end
+        i=newcontlistcatscnormi(ki)
+        j=newcontlistcatscnormj(ki)

 
 !        print *,"I am in EVDW",i
       itypi=iabs(itype(i,1))
 
 !        print *,"I am in EVDW",i
       itypi=iabs(itype(i,1))

@@ -23823,7 +23827,7 @@ C !!!!!!!! NIE CZYTANE !!!!!!!!!!!
       dyi=dc_norm(2,nres+i)
       dzi=dc_norm(3,nres+i)
       dsci_inv=vbld_inv(i+nres)
       dyi=dc_norm(2,nres+i)
       dzi=dc_norm(3,nres+i)
       dsci_inv=vbld_inv(i+nres)

-       do j=itmp+1,itmp+nres_molec(5)
+!       do j=itmp+1,itmp+nres_molec(5)

 
 ! Calculate SC interaction energy.
           itypj=iabs(itype(j,5))
 
 ! Calculate SC interaction energy.
           itypj=iabs(itype(j,5))

@@ -23848,6 +23852,9 @@ C !!!!!!!! NIE CZYTANE !!!!!!!!!!!
       zj=boxshift(zj-zi,boxzsize)
 !      write(iout,*) "xj,yj,zj", xj,yj,zj,boxxsize
 
       zj=boxshift(zj-zi,boxzsize)
 !      write(iout,*) "xj,yj,zj", xj,yj,zj,boxxsize
 

+      dxj=0.0
+      dyj=0.0
+      dzj=0.0

 !          dxj = dc_norm( 1, nres+j )
 !          dyj = dc_norm( 2, nres+j )
 !          dzj = dc_norm( 3, nres+j )
 !          dxj = dc_norm( 1, nres+j )
 !          dyj = dc_norm( 2, nres+j )
 !          dzj = dc_norm( 3, nres+j )

@@ -23957,6 +23964,11 @@ C !!!!!!!! NIE CZYTANE !!!!!!!!!!!
 ! rij holds 1/(distance of Calpha atoms)
         rrij = 1.0D0 / ( xj*xj + yj*yj + zj*zj)
         rij  = dsqrt(rrij)
 ! rij holds 1/(distance of Calpha atoms)
         rrij = 1.0D0 / ( xj*xj + yj*yj + zj*zj)
         rij  = dsqrt(rrij)

+            sss_ele_cut=sscale_ele(1.0d0/(rij))
+            sss_ele_grad=sscagrad_ele(1.0d0/(rij))
+!            print *,sss_ele_cut,sss_ele_grad,&
+!            1.0d0/(rij),r_cut_ele,rlamb_ele
+            if (sss_ele_cut.le.0.0) cycle

         CALL sc_angular
 ! this should be in elgrad_init but om's are calculated by sc_angular
 ! which in turn is used by older potentials
         CALL sc_angular
 ! this should be in elgrad_init but om's are calculated by sc_angular
 ! which in turn is used by older potentials

@@ -24007,15 +24019,15 @@ C !!!!!!!! NIE CZYTANE !!!!!!!!!!!
 !          END IF
 !#else
         evdw = evdw  &
 !          END IF
 !#else
         evdw = evdw  &

-            + evdwij
+            + evdwij*sss_ele_cut

 !#endif
         c1     = c1 * eps1 * eps2rt**2 * eps3rt**2
         fac    = -expon * (c1 + evdwij) * rij_shift
         sigder = fac * sigder
 ! Calculate distance derivative
 !#endif
         c1     = c1 * eps1 * eps2rt**2 * eps3rt**2
         fac    = -expon * (c1 + evdwij) * rij_shift
         sigder = fac * sigder
 ! Calculate distance derivative

-        gg(1) =  fac
-        gg(2) =  fac
-        gg(3) =  fac
+        gg(1) =  fac*sss_ele_cut+evdwij*sss_ele_grad
+        gg(2) =  fac*sss_ele_cut+evdwij*sss_ele_grad
+        gg(3) =  fac*sss_ele_cut+evdwij*sss_ele_grad

 !       print *,"GG(1),distance grad",gg(1)
         fac = chis1 * sqom1 + chis2 * sqom2 &
         - 2.0d0 * chis12 * om1 * om2 * om12
 !       print *,"GG(1),distance grad",gg(1)
         fac = chis1 * sqom1 + chis2 * sqom2 &
         - 2.0d0 * chis12 * om1 * om2 * om12

@@ -24034,8 +24046,9 @@ C !!!!!!!! NIE CZYTANE !!!!!!!!!!!
 
        dtop = b1cav * ((Lambf / (2.0d0 * eagle)) + (b2cav * Lambf))
        dbot = 12.0d0 * b4cav * bat * Lambf
 
        dtop = b1cav * ((Lambf / (2.0d0 * eagle)) + (b2cav * Lambf))
        dbot = 12.0d0 * b4cav * bat * Lambf

-       dFdR = ((dtop * bot - top * dbot) / botsq) * sparrow
-
+       dFdR = ((dtop * bot - top * dbot) / botsq) * sparrow*sss_ele_cut+&
+        Fcav*sss_ele_grad
+        Fcav=Fcav*sss_ele_cut

         dtop = b1cav * ((Chif / (2.0d0 * eagle)) + (b2cav * Chif))
         dbot = 12.0d0 * b4cav * bat * Chif
         eagle = Lambf * pom
         dtop = b1cav * ((Chif / (2.0d0 * eagle)) + (b2cav * Chif))
         dbot = 12.0d0 * b4cav * bat * Chif
         eagle = Lambf * pom

@@ -24075,61 +24088,47 @@ C !!!!!!!! NIE CZYTANE !!!!!!!!!!!
         isel = iabs(Qi) + 1 ! ion is always charged so  iabs(Qj)
 !        print *,i,itype(i,1),isel
         IF (isel.eq.0) THEN
         isel = iabs(Qi) + 1 ! ion is always charged so  iabs(Qj)
 !        print *,i,itype(i,1),isel
         IF (isel.eq.0) THEN

-!c! No charges - do nothing

          eheadtail = 0.0d0
          eheadtail = 0.0d0

-

         ELSE IF (isel.eq.1) THEN
         ELSE IF (isel.eq.1) THEN

-!c! Nonpolar-charge interactions

         if ((itype(i,1).eq.27).or.(itype(i,1).eq.26).or.(itype(i,1).eq.25)) then
           Qi=Qi*2
           Qij=Qij*2
          endif
         if ((itype(i,1).eq.27).or.(itype(i,1).eq.26).or.(itype(i,1).eq.25)) then
           Qi=Qi*2
           Qij=Qij*2
          endif

-

          CALL enq_cat(epol)
          eheadtail = epol
          CALL enq_cat(epol)
          eheadtail = epol

-!           eheadtail = 0.0d0
-

         ELSE IF (isel.eq.3) THEN
         ELSE IF (isel.eq.3) THEN

-!c! Dipole-charge interactions

         if ((itype(i,1).eq.27).or.(itype(i,1).eq.26).or.(itype(i,1).eq.25)) then
           Qi=Qi*2
           Qij=Qij*2
          endif
         if ((itype(i,1).eq.27).or.(itype(i,1).eq.26).or.(itype(i,1).eq.25)) then
           Qi=Qi*2
           Qij=Qij*2
          endif

-!         write(iout,*) "KURWA0",d1
-

          CALL edq_cat(ecl, elj, epol)
         eheadtail = ECL + elj + epol
          CALL edq_cat(ecl, elj, epol)
         eheadtail = ECL + elj + epol

-!           eheadtail = 0.0d0
-

         ELSE IF ((isel.eq.2)) THEN
         ELSE IF ((isel.eq.2)) THEN

-
-!c! Same charge-charge interaction ( +/+ or -/- )

         if ((itype(i,1).eq.27).or.(itype(i,1).eq.26).or.(itype(i,1).eq.25)) then
           Qi=Qi*2
           Qij=Qij*2
          endif
         if ((itype(i,1).eq.27).or.(itype(i,1).eq.26).or.(itype(i,1).eq.25)) then
           Qi=Qi*2
           Qij=Qij*2
          endif

-

          CALL eqq_cat(Ecl,Egb,Epol,Fisocav,Elj)
          eheadtail = ECL + Egb + Epol + Fisocav + Elj
          CALL eqq_cat(Ecl,Egb,Epol,Fisocav,Elj)
          eheadtail = ECL + Egb + Epol + Fisocav + Elj

-!           eheadtail = 0.0d0
-
-!          ELSE IF ((isel.eq.2.and.  &
-!               iabs(Qi).eq.1).and. &
-!               nstate(itypi,itypj).ne.1) THEN
-!c! Different charge-charge interaction ( +/- or -/+ )
-!          if ((itype(i,1).eq.27).or.(itype(i,1).eq.26).or.(itype(i,1).eq.25)) then
-!            Qi=Qi*2
-!            Qij=Qij*2
-!           endif
-!          if ((itype(j,1).eq.27).or.(itype(j,1).eq.26).or.(itype(j,1).eq.25)) then
-!            Qj=Qj*2
-!            Qij=Qij*2
-!           endif
-!
-!           CALL energy_quad(istate,eheadtail,Ecl,Egb,Epol,Fisocav,Elj,Equad)

        END IF  ! this endif ends the "catch the gly-gly" at the beggining of Fcav
        END IF  ! this endif ends the "catch the gly-gly" at the beggining of Fcav

-       else
-       write(iout,*) "not yet implemented",j,itype(j,5)
+       else ! here is water and other molecules
+        isel = iabs(Qi)+2
+!        isel=2
+!        if (isel.eq.4) isel=2
+        if (isel.eq.2) then
+         eheadtail = 0.0d0
+        else if (isel.eq.3) then
+        if ((itype(i,1).eq.27).or.(itype(i,1).eq.26).or.(itype(i,1).eq.25)) then
+          Qi=Qi*2
+          Qij=Qij*2
+         endif
+        call eqd_cat(ecl,elj,epol)
+        eheadtail = ECL + elj + epol
+        else if (isel.eq.4) then 
+        call edd_cat(ecl)
+        eheadtail = ECL
+        endif
+!       write(iout,*) "not yet implemented",j,itype(j,5)

        endif
 !!       endif ! turn off electrostatic
       evdw = evdw  + Fcav + eheadtail
        endif
 !!       endif ! turn off electrostatic
       evdw = evdw  + Fcav + eheadtail

@@ -24156,14 +24155,18 @@ C !!!!!!!! NIE CZYTANE !!!!!!!!!!!
 !c!-------------------------------------------------------------------
 !c! NAPISY KONCOWE
        END DO   ! j
 !c!-------------------------------------------------------------------
 !c! NAPISY KONCOWE
        END DO   ! j

-       END DO     ! i
+!       END DO     ! i

 !c      write (iout,*) "Number of loop steps in EGB:",ind
 !c      energy_dec=.false.
 !              print *,"EVDW KURW",evdw,nres
 !!!        return
    17   continue
 !      go to 23
 !c      write (iout,*) "Number of loop steps in EGB:",ind
 !c      energy_dec=.false.
 !              print *,"EVDW KURW",evdw,nres
 !!!        return
    17   continue
 !      go to 23

-      do i=ibond_start,ibond_end
+!      do i=ibond_start,ibond_end
+
+      do ki=g_listcatpnorm_start,g_listcatpnorm_end
+        i=newcontlistcatpnormi(ki)
+        j=newcontlistcatpnormj(ki)

 
 !        print *,"I am in EVDW",i
       itypi=10 ! the peptide group parameters are for glicine
 
 !        print *,"I am in EVDW",i
       itypi=10 ! the peptide group parameters are for glicine

@@ -24179,7 +24182,7 @@ C !!!!!!!! NIE CZYTANE !!!!!!!!!!!
       dyi=dc_norm(2,i)
       dzi=dc_norm(3,i)
       dsci_inv=vbld_inv(i+1)/2.0
       dyi=dc_norm(2,i)
       dzi=dc_norm(3,i)
       dsci_inv=vbld_inv(i+1)/2.0

-       do j=itmp+1,itmp+nres_molec(5)
+!       do j=itmp+1,itmp+nres_molec(5)

 
 ! Calculate SC interaction energy.
           itypj=iabs(itype(j,5))
 
 ! Calculate SC interaction energy.
           itypj=iabs(itype(j,5))

@@ -24304,15 +24307,22 @@ C !!!!!!!! NIE CZYTANE !!!!!!!!!!!
         dCAVdOM1  = 0.0d0
         dCAVdOM2  = 0.0d0
         dCAVdOM12 = 0.0d0
         dCAVdOM1  = 0.0d0
         dCAVdOM2  = 0.0d0
         dCAVdOM12 = 0.0d0

-        dscj_inv = vbld_inv(j+nres)
+        dscj_inv = 0.0d0 ! vbld_inv(j+nres)

 !          print *,i,j,dscj_inv,dsci_inv
 ! rij holds 1/(distance of Calpha atoms)
         rrij = 1.0D0 / ( xj*xj + yj*yj + zj*zj)
         rij  = dsqrt(rrij)
 !          print *,i,j,dscj_inv,dsci_inv
 ! rij holds 1/(distance of Calpha atoms)
         rrij = 1.0D0 / ( xj*xj + yj*yj + zj*zj)
         rij  = dsqrt(rrij)

+            sss_ele_cut=sscale_ele(1.0d0/(rij))
+            sss_ele_grad=sscagrad_ele(1.0d0/(rij))
+!            print *,sss_ele_cut,sss_ele_grad,&
+!            1.0d0/(rij),r_cut_ele,rlamb_ele
+            if (sss_ele_cut.le.0.0) cycle

         CALL sc_angular
 ! this should be in elgrad_init but om's are calculated by sc_angular
 ! which in turn is used by older potentials
 ! om = omega, sqom = om^2
         CALL sc_angular
 ! this should be in elgrad_init but om's are calculated by sc_angular
 ! which in turn is used by older potentials
 ! om = omega, sqom = om^2

+        om2=0.0d0
+        om12=0.0d0

         sqom1  = om1 * om1
         sqom2  = om2 * om2
         sqom12 = om12 * om12
         sqom1  = om1 * om1
         sqom2  = om2 * om2
         sqom12 = om12 * om12

@@ -24356,15 +24366,15 @@ C !!!!!!!! NIE CZYTANE !!!!!!!!!!!
 !          END IF
 !#else
         evdw = evdw  &
 !          END IF
 !#else
         evdw = evdw  &

-            + evdwij
+            + evdwij*sss_ele_cut

 !#endif
         c1     = c1 * eps1 * eps2rt**2 * eps3rt**2
         fac    = -expon * (c1 + evdwij) * rij_shift
         sigder = fac * sigder
 ! Calculate distance derivative
 !#endif
         c1     = c1 * eps1 * eps2rt**2 * eps3rt**2
         fac    = -expon * (c1 + evdwij) * rij_shift
         sigder = fac * sigder
 ! Calculate distance derivative

-        gg(1) =  fac
-        gg(2) =  fac
-        gg(3) =  fac
+        gg(1) =  fac*sss_ele_cut+evdwij*sss_ele_grad
+        gg(2) =  fac*sss_ele_cut+evdwij*sss_ele_grad
+        gg(3) =  fac*sss_ele_cut+evdwij*sss_ele_grad

 
         fac = chis1 * sqom1 + chis2 * sqom2 &
         - 2.0d0 * chis12 * om1 * om2 * om12
 
         fac = chis1 * sqom1 + chis2 * sqom2 &
         - 2.0d0 * chis12 * om1 * om2 * om12

@@ -24385,20 +24395,24 @@ C !!!!!!!! NIE CZYTANE !!!!!!!!!!!
 
        dtop = b1cav * ((Lambf / (2.0d0 * eagle)) + (b2cav * Lambf))
        dbot = 12.0d0 * b4cav * bat * Lambf
 
        dtop = b1cav * ((Lambf / (2.0d0 * eagle)) + (b2cav * Lambf))
        dbot = 12.0d0 * b4cav * bat * Lambf

-       dFdR = ((dtop * bot - top * dbot) / botsq) * sparrow
-
+       dFdR = ((dtop * bot - top * dbot) / botsq) * sparrow*sss_ele_cut+&
+          Fcav*sss_ele_grad
+        Fcav=Fcav*sss_ele_cut

         dtop = b1cav * ((Chif / (2.0d0 * eagle)) + (b2cav * Chif))
         dbot = 12.0d0 * b4cav * bat * Chif
         eagle = Lambf * pom
         dFdOM1  = -(chis1 * om1 - chis12 * om2 * om12) / (eagle)
         dtop = b1cav * ((Chif / (2.0d0 * eagle)) + (b2cav * Chif))
         dbot = 12.0d0 * b4cav * bat * Chif
         eagle = Lambf * pom
         dFdOM1  = -(chis1 * om1 - chis12 * om2 * om12) / (eagle)

+

         dFdOM2  = -(chis2 * om2 - chis12 * om1 * om12) / (eagle)
         dFdOM12 = chis12 * (chis1 * om1 * om12 - om2) &
             * (chis2 * om2 * om12 - om1) / (eagle * pom)
 
         dFdL = ((dtop * bot - top * dbot) / botsq)
         dCAVdOM1  = dFdL * ( dFdOM1 )
         dFdOM2  = -(chis2 * om2 - chis12 * om1 * om12) / (eagle)
         dFdOM12 = chis12 * (chis1 * om1 * om12 - om2) &
             * (chis2 * om2 * om12 - om1) / (eagle * pom)
 
         dFdL = ((dtop * bot - top * dbot) / botsq)
         dCAVdOM1  = dFdL * ( dFdOM1 )

-        dCAVdOM2  = dFdL * ( dFdOM2 )
-        dCAVdOM12 = dFdL * ( dFdOM12 )
+!        dCAVdOM2  = dFdL * ( dFdOM2 )
+!        dCAVdOM12 = dFdL * ( dFdOM12 )
+        dCAVdOM2=0.0d0
+        dCAVdOM12=0.0d0

 
        DO k= 1, 3
       ertail(k) = Rtail_distance(k)/Rtail
 
        DO k= 1, 3
       ertail(k) = Rtail_distance(k)/Rtail

@@ -24433,8 +24447,11 @@ C !!!!!!!! NIE CZYTANE !!!!!!!!!!!
 !           eheadtail = 0.0d0
       else
 !HERE WATER and other types of molecules solvents will be added
 !           eheadtail = 0.0d0
       else
 !HERE WATER and other types of molecules solvents will be added

-      write(iout,*) "not yet implemented"
+!      write(iout,*) "not yet implemented"
+         CALL edd_cat_pep(ecl)
+         eheadtail=ecl

 !      CALL edd_cat_pep
 !      CALL edd_cat_pep

+!      eheadtail=0.0d0

       endif
       evdw = evdw  + Fcav + eheadtail
 !      if (evdw.gt.1.0d6) then
       endif
       evdw = evdw  + Fcav + eheadtail
 !      if (evdw.gt.1.0d6) then

@@ -24455,7 +24472,7 @@ C !!!!!!!! NIE CZYTANE !!!!!!!!!!!
 !c!-------------------------------------------------------------------
 !c! NAPISY KONCOWE
        END DO   ! j
 !c!-------------------------------------------------------------------
 !c! NAPISY KONCOWE
        END DO   ! j

-       END DO     ! i
+!       END DO     ! i

 !c      write (iout,*) "Number of loop steps in EGB:",ind
 !c      energy_dec=.false.
 !              print *,"EVDW KURW",evdw,nres
 !c      write (iout,*) "Number of loop steps in EGB:",ind
 !c      energy_dec=.false.
 !              print *,"EVDW KURW",evdw,nres

@@ -24505,6 +24522,7 @@ C !!!!!!!! NIE CZYTANE !!!!!!!!!!!
 !        do i=1,nres_molec(1)-1  ! loop over all peptide groups needs parralelization
       do i=ibond_start,ibond_end
 !         cycle
 !        do i=1,nres_molec(1)-1  ! loop over all peptide groups needs parralelization
       do i=ibond_start,ibond_end
 !         cycle

+       

        if ((itype(i,1).eq.ntyp1).or.(itype(i+1,1).eq.ntyp1)) cycle ! leave dummy atoms
       xi=0.5d0*(c(1,i)+c(1,i+1))
       yi=0.5d0*(c(2,i)+c(2,i+1))
        if ((itype(i,1).eq.ntyp1).or.(itype(i+1,1).eq.ntyp1)) cycle ! leave dummy atoms
       xi=0.5d0*(c(1,i)+c(1,i+1))
       yi=0.5d0*(c(2,i)+c(2,i+1))

@@ -26818,7 +26836,7 @@ C !!!!!!!! NIE CZYTANE !!!!!!!!!!!
       real(kind=8) :: xj_safe,yj_safe,zj_safe,xj_temp,yj_temp,zj_temp,&
                 dist_temp, dist_init,ssgradlipi,ssgradlipj, &
                 sslipi,sslipj,faclip,alpha_sco
       real(kind=8) :: xj_safe,yj_safe,zj_safe,xj_temp,yj_temp,zj_temp,&
                 dist_temp, dist_init,ssgradlipi,ssgradlipj, &
                 sslipi,sslipj,faclip,alpha_sco

-      integer :: ii
+      integer :: ii,icont

       real(kind=8) :: fracinbuf
        real (kind=8) :: escpho
        real (kind=8),dimension(4):: ener
       real(kind=8) :: fracinbuf
        real (kind=8) :: escpho
        real (kind=8),dimension(4):: ener

@@ -26839,8 +26857,12 @@ C !!!!!!!! NIE CZYTANE !!!!!!!!!!!
        sss_ele_cut=1.0d0
        countss=0
 !       print *,"EVDW KURW",evdw,nres
        sss_ele_cut=1.0d0
        countss=0
 !       print *,"EVDW KURW",evdw,nres

-      do i=iatsc_s,iatsc_e
+!      do i=iatsc_s,iatsc_e

 !        print *,"I am in EVDW",i
 !        print *,"I am in EVDW",i

+      do icont=g_listscsc_start,g_listscsc_end
+      i=newcontlisti(icont)
+      j=newcontlistj(icont)
+

       itypi=iabs(itype(i,1))
 !        if (i.ne.47) cycle
       if (itypi.eq.ntyp1) cycle
       itypi=iabs(itype(i,1))
 !        if (i.ne.47) cycle
       if (itypi.eq.ntyp1) cycle

@@ -26862,8 +26884,8 @@ C !!!!!!!! NIE CZYTANE !!!!!!!!!!!
 !
 ! Calculate SC interaction energy.
 !
 !
 ! Calculate SC interaction energy.
 !

-      do iint=1,nint_gr(i)
-        do j=istart(i,iint),iend(i,iint)
+!      do iint=1,nint_gr(i)
+!        do j=istart(i,iint),iend(i,iint)

 !             print *,"JA PIER",i,j,iint,istart(i,iint),iend(i,iint)
           IF (dyn_ss_mask(i).and.dyn_ss_mask(j)) THEN
             call dyn_ssbond_ene(i,j,evdwij,countss)
 !             print *,"JA PIER",i,j,iint,istart(i,iint),iend(i,iint)
           IF (dyn_ss_mask(i).and.dyn_ss_mask(j)) THEN
             call dyn_ssbond_ene(i,j,evdwij,countss)

@@ -27041,6 +27063,12 @@ C !!!!!!!! NIE CZYTANE !!!!!!!!!!!
 ! rij holds 1/(distance of Calpha atoms)
         rrij = 1.0D0 / ( xj*xj + yj*yj + zj*zj)
         rij  = dsqrt(rrij)
 ! rij holds 1/(distance of Calpha atoms)
         rrij = 1.0D0 / ( xj*xj + yj*yj + zj*zj)
         rij  = dsqrt(rrij)

+            sss_ele_cut=sscale_ele(1.0d0/(rij))
+            sss_ele_grad=sscagrad_ele(1.0d0/(rij))
+!            print *,sss_ele_cut,sss_ele_grad,&
+!            1.0d0/(rij),r_cut_ele,rlamb_ele
+            if (sss_ele_cut.le.0.0) cycle
+

 !----------------------------
         CALL sc_angular
 ! this should be in elgrad_init but om's are calculated by sc_angular
 !----------------------------
         CALL sc_angular
 ! this should be in elgrad_init but om's are calculated by sc_angular

@@ -27082,7 +27110,7 @@ C !!!!!!!! NIE CZYTANE !!!!!!!!!!!
 !          END IF
 !#else
         evdw = evdw  &
 !          END IF
 !#else
         evdw = evdw  &

-            + evdwij
+            + evdwij*sss_ele_cut

 !#endif
 
         c1     = c1 * eps1 * eps2rt**2 * eps3rt**2
 !#endif
 
         c1     = c1 * eps1 * eps2rt**2 * eps3rt**2

@@ -27090,9 +27118,9 @@ C !!!!!!!! NIE CZYTANE !!!!!!!!!!!
         sigder = fac * sigder
 !          fac    = rij * fac
 ! Calculate distance derivative
         sigder = fac * sigder
 !          fac    = rij * fac
 ! Calculate distance derivative

-        gg(1) =  fac
-        gg(2) =  fac
-        gg(3) =  fac
+        gg(1) =  fac*sss_ele_cut+evdwij*sss_ele_grad
+        gg(2) =  fac*sss_ele_cut+evdwij*sss_ele_grad
+        gg(3) =  fac*sss_ele_cut+evdwij*sss_ele_grad

 !          if (b2.gt.0.0) then
         fac = chis1 * sqom1 + chis2 * sqom2 &
         - 2.0d0 * chis12 * om1 * om2 * om12
 !          if (b2.gt.0.0) then
         fac = chis1 * sqom1 + chis2 * sqom2 &
         - 2.0d0 * chis12 * om1 * om2 * om12

@@ -27117,8 +27145,9 @@ C !!!!!!!! NIE CZYTANE !!!!!!!!!!!
 
        dtop = b1cav * ((Lambf / (2.0d0 * eagle)) + (b2cav * Lambf))
        dbot = 12.0d0 * b4cav * bat * Lambf
 
        dtop = b1cav * ((Lambf / (2.0d0 * eagle)) + (b2cav * Lambf))
        dbot = 12.0d0 * b4cav * bat * Lambf

-       dFdR = ((dtop * bot - top * dbot) / botsq) * sparrow
-
+       dFdR = ((dtop * bot - top * dbot) / botsq) * sparrow*sss_ele_cut&
+            +Fcav*sss_ele_grad
+        Fcav=Fcav*sss

         dtop = b1cav * ((Chif / (2.0d0 * eagle)) + (b2cav * Chif))
         dbot = 12.0d0 * b4cav * bat * Chif
         eagle = Lambf * pom
         dtop = b1cav * ((Chif / (2.0d0 * eagle)) + (b2cav * Chif))
         dbot = 12.0d0 * b4cav * bat * Chif
         eagle = Lambf * pom

@@ -27295,8 +27324,8 @@ C !!!!!!!! NIE CZYTANE !!!!!!!!!!!
        END IF
 !c!-------------------------------------------------------------------
 !c! NAPISY KONCOWE
        END IF
 !c!-------------------------------------------------------------------
 !c! NAPISY KONCOWE

-       END DO   ! j
-      END DO    ! iint
+      ! END DO   ! j
+      !END DO    ! iint

        END DO     ! i
 !c      write (iout,*) "Number of loop steps in EGB:",ind
 !c      energy_dec=.false.
        END DO     ! i
 !c      write (iout,*) "Number of loop steps in EGB:",ind
 !c      energy_dec=.false.

@@ -27348,10 +27377,11 @@ C !!!!!!!! NIE CZYTANE !!!!!!!!!!!
 !c! Coulomb electrostatic interaction
        Ecl = (332.0d0 * Qij) / Rhead
 !c! derivative of Ecl is Gcl...
 !c! Coulomb electrostatic interaction
        Ecl = (332.0d0 * Qij) / Rhead
 !c! derivative of Ecl is Gcl...

-       dGCLdR = (-332.0d0 * Qij ) / Rhead_sq
+       dGCLdR = (-332.0d0 * Qij ) / Rhead_sq*sss_ele_cut+ECL*sss_ele_grad

        dGCLdOM1 = 0.0d0
        dGCLdOM2 = 0.0d0
        dGCLdOM12 = 0.0d0
        dGCLdOM1 = 0.0d0
        dGCLdOM2 = 0.0d0
        dGCLdOM12 = 0.0d0

+       ECL=ECL*sss_ele_grad

        ee0 = dexp(-( Rhead_sq ) / (4.0d0 * a12sq))
        Fgb = sqrt( ( Rhead_sq ) + a12sq * ee0)
        debkap=debaykap(itypi,itypj)
        ee0 = dexp(-( Rhead_sq ) / (4.0d0 * a12sq))
        Fgb = sqrt( ( Rhead_sq ) + a12sq * ee0)
        debkap=debaykap(itypi,itypj)

@@ -27364,7 +27394,8 @@ C !!!!!!!! NIE CZYTANE !!!!!!!!!!!
        -(332.0d0 * Qij *&
       (dexp(-debkap*Fgb)*debkap/eps_out))/ Fgb
        dFGBdR = ( Rhead * ( 2.0d0 - (0.5d0 * ee0) ) )/ ( 2.0d0 * Fgb )
        -(332.0d0 * Qij *&
       (dexp(-debkap*Fgb)*debkap/eps_out))/ Fgb
        dFGBdR = ( Rhead * ( 2.0d0 - (0.5d0 * ee0) ) )/ ( 2.0d0 * Fgb )

-       dGGBdR = dGGBdFGB * dFGBdR
+       dGGBdR = dGGBdFGB * dFGBdR*sss_ele_cut+Egb*sss_ele_grad
+       Egb=Egb*sss_ele_cut

 !c!-------------------------------------------------------------------
 !c! Fisocav - isotropic cavity creation term
 !c! or "how much energy it costs to put charged head in water"
 !c!-------------------------------------------------------------------
 !c! Fisocav - isotropic cavity creation term
 !c! or "how much energy it costs to put charged head in water"

@@ -27412,9 +27443,9 @@ C !!!!!!!! NIE CZYTANE !!!!!!!!!!!
             * ( 2.0d0 - 0.5d0 * ee1) ) / ( 2.0d0 * fgb1 )
        dFGBdOM1 = (((R2 * R2 * chi2 * om1) / (MomoFac2 * MomoFac2))&
             * ( 2.0d0 - 0.5d0 * ee2) ) / ( 2.0d0 * fgb2 )
             * ( 2.0d0 - 0.5d0 * ee1) ) / ( 2.0d0 * fgb1 )
        dFGBdOM1 = (((R2 * R2 * chi2 * om1) / (MomoFac2 * MomoFac2))&
             * ( 2.0d0 - 0.5d0 * ee2) ) / ( 2.0d0 * fgb2 )

-       dPOLdR1 = dPOLdFGB1 * dFGBdR1
+       dPOLdR1 = dPOLdFGB1 * dFGBdR1*sss_ele_cut

 !c!       dPOLdR1 = 0.0d0
 !c!       dPOLdR1 = 0.0d0

-       dPOLdR2 = dPOLdFGB2 * dFGBdR2
+       dPOLdR2 = dPOLdFGB2 * dFGBdR2*sss_ele_cut

 !c!       dPOLdR2 = 0.0d0
        dPOLdOM1 = dPOLdFGB2 * dFGBdOM1
 !c!       dPOLdOM1 = 0.0d0
 !c!       dPOLdR2 = 0.0d0
        dPOLdOM1 = dPOLdFGB2 * dFGBdOM1
 !c!       dPOLdOM1 = 0.0d0

@@ -27427,7 +27458,10 @@ C !!!!!!!! NIE CZYTANE !!!!!!!!!!!
        Elj = 4.0d0 * eps_head * pom * (pom-1.0d0)
 !c! derivative of Elj is Glj
        dGLJdR = 4.0d0 * eps_head*(((-12.0d0*pis**12.0d0)/(Rhead**13.0d0))&
        Elj = 4.0d0 * eps_head * pom * (pom-1.0d0)
 !c! derivative of Elj is Glj
        dGLJdR = 4.0d0 * eps_head*(((-12.0d0*pis**12.0d0)/(Rhead**13.0d0))&

-           +  ((  6.0d0*pis**6.0d0) /(Rhead**7.0d0)))
+           +  ((  6.0d0*pis**6.0d0) /(Rhead**7.0d0)))*sss_ele_cut+&
+         (ELJ+epol)*sss_ele_grad
+        epol=epol*sss_ele_cut
+        Elj=Elj*sss_ele_cut

 !c!-------------------------------------------------------------------
 !c! Return the results
 !c! These things do the dRdX derivatives, that is
 !c!-------------------------------------------------------------------
 !c! Return the results
 !c! These things do the dRdX derivatives, that is

@@ -27538,7 +27572,8 @@ C !!!!!!!! NIE CZYTANE !!!!!!!!!!!
 !c! Coulomb electrostatic interaction
        Ecl = (332.0d0 * Qij) / Rhead
 !c! derivative of Ecl is Gcl...
 !c! Coulomb electrostatic interaction
        Ecl = (332.0d0 * Qij) / Rhead
 !c! derivative of Ecl is Gcl...

-       dGCLdR = (-332.0d0 * Qij ) / Rhead_sq
+       dGCLdR = (-332.0d0 * Qij ) / Rhead_sq*sss_ele_cut+ECL*sss_ele_grad
+       ECL=ECL*sss_ele_cut

        dGCLdOM1 = 0.0d0
        dGCLdOM2 = 0.0d0
        dGCLdOM12 = 0.0d0
        dGCLdOM1 = 0.0d0
        dGCLdOM2 = 0.0d0
        dGCLdOM12 = 0.0d0

@@ -27556,7 +27591,8 @@ C !!!!!!!! NIE CZYTANE !!!!!!!!!!!
        -(332.0d0 * Qij *&
       (dexp(-debkap*Fgb)*debkap/eps_out))/ Fgb
        dFGBdR = ( Rhead * ( 2.0d0 - (0.5d0 * ee0) ) )/ ( 2.0d0 * Fgb )
        -(332.0d0 * Qij *&
       (dexp(-debkap*Fgb)*debkap/eps_out))/ Fgb
        dFGBdR = ( Rhead * ( 2.0d0 - (0.5d0 * ee0) ) )/ ( 2.0d0 * Fgb )

-       dGGBdR = dGGBdFGB * dFGBdR
+       dGGBdR = dGGBdFGB * dFGBdR*sss_ele_cut+Egb*sss_ele_grad
+       Egb=Egb*sss_ele_grad

 !c!-------------------------------------------------------------------
 !c! Fisocav - isotropic cavity creation term
 !c! or "how much energy it costs to put charged head in water"
 !c!-------------------------------------------------------------------
 !c! Fisocav - isotropic cavity creation term
 !c! or "how much energy it costs to put charged head in water"

@@ -27577,7 +27613,9 @@ C !!!!!!!! NIE CZYTANE !!!!!!!!!!!
 !c! Derivative of Fisocav is GCV...
        dtop = al1 * ((1.0d0 / (2.0d0 * dsqrt(pom))) + al2)
        dbot = 12.0d0 * al4 * pom ** 11.0d0
 !c! Derivative of Fisocav is GCV...
        dtop = al1 * ((1.0d0 / (2.0d0 * dsqrt(pom))) + al2)
        dbot = 12.0d0 * al4 * pom ** 11.0d0

-       dGCVdR = ((dtop * bot - top * dbot) / botsq) * csig
+       dGCVdR = ((dtop * bot - top * dbot) / botsq) * csig*sss_ele_cut&
+               +FisoCav*sss_ele_grad
+        FisoCav=FisoCav*sss_ele_cut

 !c!-------------------------------------------------------------------
 !c! Epol
 !c! Polarization energy - charged heads polarize hydrophobic "neck"
 !c!-------------------------------------------------------------------
 !c! Epol
 !c! Polarization energy - charged heads polarize hydrophobic "neck"

@@ -27604,13 +27642,14 @@ C !!!!!!!! NIE CZYTANE !!!!!!!!!!!
             * ( 2.0d0 - 0.5d0 * ee1) ) / ( 2.0d0 * fgb1 )
        dFGBdOM1 = (((R2 * R2 * chi2 * om1) / (MomoFac2 * MomoFac2))&
             * ( 2.0d0 - 0.5d0 * ee2) ) / ( 2.0d0 * fgb2 )
             * ( 2.0d0 - 0.5d0 * ee1) ) / ( 2.0d0 * fgb1 )
        dFGBdOM1 = (((R2 * R2 * chi2 * om1) / (MomoFac2 * MomoFac2))&
             * ( 2.0d0 - 0.5d0 * ee2) ) / ( 2.0d0 * fgb2 )

-       dPOLdR1 = dPOLdFGB1 * dFGBdR1
+       dPOLdR1 = dPOLdFGB1 * dFGBdR1!*sss_ele_cut+epol*sss_ele_grad

 !c!       dPOLdR1 = 0.0d0
 !c!       dPOLdR1 = 0.0d0

-       dPOLdR2 = dPOLdFGB2 * dFGBdR2
+       dPOLdR2 = dPOLdFGB2 * dFGBdR2!*sss_ele_cut+epol*sss_ele_grad

 !c!       dPOLdR2 = 0.0d0
        dPOLdOM1 = dPOLdFGB2 * dFGBdOM1
 !c!       dPOLdOM1 = 0.0d0
        dPOLdOM2 = dPOLdFGB1 * dFGBdOM2
 !c!       dPOLdR2 = 0.0d0
        dPOLdOM1 = dPOLdFGB2 * dFGBdOM1
 !c!       dPOLdOM1 = 0.0d0
        dPOLdOM2 = dPOLdFGB1 * dFGBdOM2

+!       epol=epol*sss_ele_cut

 !c!       dPOLdOM2 = 0.0d0
 !c!-------------------------------------------------------------------
 !c! Elj
 !c!       dPOLdOM2 = 0.0d0
 !c!-------------------------------------------------------------------
 !c! Elj

@@ -27619,7 +27658,10 @@ C !!!!!!!! NIE CZYTANE !!!!!!!!!!!
        Elj = 4.0d0 * eps_head * pom * (pom-1.0d0)
 !c! derivative of Elj is Glj
        dGLJdR = 4.0d0 * eps_head*(((-12.0d0*pis**12.0d0)/(Rhead**13.0d0))&
        Elj = 4.0d0 * eps_head * pom * (pom-1.0d0)
 !c! derivative of Elj is Glj
        dGLJdR = 4.0d0 * eps_head*(((-12.0d0*pis**12.0d0)/(Rhead**13.0d0))&

-           +  ((  6.0d0*pis**6.0d0) /(Rhead**7.0d0)))
+           +  ((  6.0d0*pis**6.0d0) /(Rhead**7.0d0)))*sss_ele_cut&
+           +(Elj+epol)*sss_ele_grad
+       Elj=Elj*sss_ele_cut
+       epol=epol*sss_ele_cut

 !c!-------------------------------------------------------------------
 !c! Return the results
 !c! These things do the dRdX derivatives, that is
 !c!-------------------------------------------------------------------
 !c! Return the results
 !c! These things do the dRdX derivatives, that is

@@ -27737,15 +27779,15 @@ C !!!!!!!! NIE CZYTANE !!!!!!!!!!!
       dcosom2(k) = rij * (dc_norm(k,nres+j) - om2 * erij(k))
       gg(k) = gg(k) + eom1 * dcosom1(k) + eom2 * dcosom2(k)
 !c! this acts on hydrophobic center of interaction
       dcosom2(k) = rij * (dc_norm(k,nres+j) - om2 * erij(k))
       gg(k) = gg(k) + eom1 * dcosom1(k) + eom2 * dcosom2(k)
 !c! this acts on hydrophobic center of interaction

-      gvdwx(k,i)= gvdwx(k,i) - gg(k) &
+      gvdwx(k,i)= gvdwx(k,i) - gg(k)*sss_ele_cut &

               + (eom12*(dc_norm(k,nres+j)-om12*dc_norm(k,nres+i))&
               + (eom12*(dc_norm(k,nres+j)-om12*dc_norm(k,nres+i))&

-              + eom1*(erij(k)-om1*dc_norm(k,nres+i)))*dsci_inv
-      gvdwx(k,j)= gvdwx(k,j) + gg(k) &
+              + eom1*(erij(k)-om1*dc_norm(k,nres+i)))*dsci_inv*sss_ele_cut
+      gvdwx(k,j)= gvdwx(k,j) + gg(k)*sss_ele_cut &

               + (eom12*(dc_norm(k,nres+i)-om12*dc_norm(k,nres+j))&
               + (eom12*(dc_norm(k,nres+i)-om12*dc_norm(k,nres+j))&

-              + eom2*(erij(k)-om2*dc_norm(k,nres+j)))*dscj_inv
+              + eom2*(erij(k)-om2*dc_norm(k,nres+j)))*dscj_inv*sss_ele_cut

 !c! this acts on Calpha
 !c! this acts on Calpha

-      gvdwc(k,i)=gvdwc(k,i)-gg(k)
-      gvdwc(k,j)=gvdwc(k,j)+gg(k)
+      gvdwc(k,i)=gvdwc(k,i)-gg(k)*sss_ele_cut
+      gvdwc(k,j)=gvdwc(k,j)+gg(k)*sss_ele_cut

        END DO
 !c! sc_grad is done, now we will compute 
        eheadtail = 0.0d0
        END DO
 !c! sc_grad is done, now we will compute 
        eheadtail = 0.0d0

@@ -27816,7 +27858,8 @@ C !!!!!!!! NIE CZYTANE !!!!!!!!!!!
 !c!        Ecl = 0.0d0
 !c!        write (*,*) "Ecl = ", Ecl
 !c! derivative of Ecl is Gcl...
 !c!        Ecl = 0.0d0
 !c!        write (*,*) "Ecl = ", Ecl
 !c! derivative of Ecl is Gcl...

-      dGCLdR = (-332.0d0 * Qij ) / (Rhead_sq * eps_in)
+      dGCLdR = (-332.0d0 * Qij ) / (Rhead_sq * eps_in)*sss_ele_cut+ECL*sss_ele_grad
+       ECL=ecl*sss_ele_cut

 !c!        dGCLdR = 0.0d0
       dGCLdOM1 = 0.0d0
       dGCLdOM2 = 0.0d0
 !c!        dGCLdR = 0.0d0
       dGCLdOM1 = 0.0d0
       dGCLdOM2 = 0.0d0

@@ -27840,7 +27883,8 @@ C !!!!!!!! NIE CZYTANE !!!!!!!!!!!
       dGGBdFGB = -(-332.0d0 * Qij * eps_inout_fac) / (Fgb * Fgb)
       dFGBdR = ( Rhead * ( 2.0d0 - (0.5d0 * ee0) ) )&
              / ( 2.0d0 * Fgb )
       dGGBdFGB = -(-332.0d0 * Qij * eps_inout_fac) / (Fgb * Fgb)
       dFGBdR = ( Rhead * ( 2.0d0 - (0.5d0 * ee0) ) )&
              / ( 2.0d0 * Fgb )

-      dGGBdR = dGGBdFGB * dFGBdR
+      dGGBdR = dGGBdFGB * dFGBdR*sss_ele_cut+Egb*sss_ele_grad
+      Egb=Egb*sss_ele_cut

 !c!        dGGBdR = 0.0d0
 !c!-------------------------------------------------------------------
 !c! Fisocav - isotropic cavity creation term
 !c!        dGGBdR = 0.0d0
 !c!-------------------------------------------------------------------
 !c! Fisocav - isotropic cavity creation term

@@ -27851,7 +27895,9 @@ C !!!!!!!! NIE CZYTANE !!!!!!!!!!!
       FisoCav = top / bot
       dtop = al1 * ((1.0d0 / (2.0d0 * dsqrt(pom))) + al2)
       dbot = 12.0d0 * al4 * pom ** 11.0d0
       FisoCav = top / bot
       dtop = al1 * ((1.0d0 / (2.0d0 * dsqrt(pom))) + al2)
       dbot = 12.0d0 * al4 * pom ** 11.0d0

-      dGCVdR = ((dtop * bot - top * dbot) / botsq) * csig
+      dGCVdR = ((dtop * bot - top * dbot) / botsq) * csig*sss_ele_cut+FisoCav*sss_ele_grad
+      FisoCav=FisoCav*sss_ele_cut
+      

 !c!        dGCVdR = 0.0d0
 !c!-------------------------------------------------------------------
 !c! Polarization energy
 !c!        dGCVdR = 0.0d0
 !c!-------------------------------------------------------------------
 !c! Polarization energy

@@ -27884,9 +27930,9 @@ C !!!!!!!! NIE CZYTANE !!!!!!!!!!!
       dFGBdOM1 = (((R2 * R2 * chi2 * om1) / (MomoFac2 * MomoFac2)) &
              * ( 2.0d0 - 0.5d0 * ee2) ) &
              / ( 2.0d0 * fgb2 )
       dFGBdOM1 = (((R2 * R2 * chi2 * om1) / (MomoFac2 * MomoFac2)) &
              * ( 2.0d0 - 0.5d0 * ee2) ) &
              / ( 2.0d0 * fgb2 )

-      dPOLdR1 = dPOLdFGB1 * dFGBdR1
+      dPOLdR1 = dPOLdFGB1 * dFGBdR1*sss_ele_cut

 !c!        dPOLdR1 = 0.0d0
 !c!        dPOLdR1 = 0.0d0

-      dPOLdR2 = dPOLdFGB2 * dFGBdR2
+      dPOLdR2 = dPOLdFGB2 * dFGBdR2*sss_ele_cut

 !c!        dPOLdR2 = 0.0d0
       dPOLdOM1 = dPOLdFGB2 * dFGBdOM1
 !c!        dPOLdOM1 = 0.0d0
 !c!        dPOLdR2 = 0.0d0
       dPOLdOM1 = dPOLdFGB2 * dFGBdOM1
 !c!        dPOLdOM1 = 0.0d0

@@ -27897,7 +27943,10 @@ C !!!!!!!! NIE CZYTANE !!!!!!!!!!!
 !c! derivative of Elj is Glj
       dGLJdR = 4.0d0 * eps_head &
           * (((-12.0d0*pis**12.0d0)/(Rhead**13.0d0)) &
 !c! derivative of Elj is Glj
       dGLJdR = 4.0d0 * eps_head &
           * (((-12.0d0*pis**12.0d0)/(Rhead**13.0d0)) &

-          +  ((  6.0d0*pis**6.0d0) /(Rhead**7.0d0)))
+          +  ((  6.0d0*pis**6.0d0) /(Rhead**7.0d0)))*sss_ele_cut+&
+          (epol+Elj)*sss_ele_grad
+      Elj=Elj*sss_ele_cut
+      epol=epol*sss_ele_cut

 !c!        dGLJdR = 0.0d0
 !c!-------------------------------------------------------------------
 !c! Equad
 !c!        dGLJdR = 0.0d0
 !c!-------------------------------------------------------------------
 !c! Equad

@@ -27910,7 +27959,9 @@ C !!!!!!!! NIE CZYTANE !!!!!!!!!!!
       Equad = fac * Beta1
 !c!        Equad = 0.0d0
 !c! derivative of Equad...
       Equad = fac * Beta1
 !c!        Equad = 0.0d0
 !c! derivative of Equad...

-      dQUADdR = ((2.5d0 * Wqd * Beta1) / (Fgb**6.0d0)) * dFGBdR
+      dQUADdR = ((2.5d0 * Wqd * Beta1) / (Fgb**6.0d0)) * dFGBdR*sss_ele_cut&
+          + Equad*sss_ele_grad
+      Equad=Equad*sss_ele_cut

 !c!        dQUADdR = 0.0d0
       dQUADdOM1 = fac* (-75.0d0*om1 + 315.0d0*om1*sqom2 - 45.0d0*om2*om12)
 !c!        dQUADdOM1 = 0.0d0
 !c!        dQUADdR = 0.0d0
       dQUADdOM1 = fac* (-75.0d0*om1 + 315.0d0*om1*sqom2 - 45.0d0*om2*om12)
 !c!        dQUADdOM1 = 0.0d0

@@ -27932,7 +27983,7 @@ C !!!!!!!! NIE CZYTANE !!!!!!!!!!!
       DO k = 1, 3
        dcosom1(k) = rij * (dc_norm(k,nres+i) - om1 * erij(k))
        dcosom2(k) = rij * (dc_norm(k,nres+j) - om2 * erij(k))
       DO k = 1, 3
        dcosom1(k) = rij * (dc_norm(k,nres+i) - om1 * erij(k))
        dcosom2(k) = rij * (dc_norm(k,nres+j) - om2 * erij(k))

-       tuna(k) = eom1 * dcosom1(k) + eom2 * dcosom2(k)
+       tuna(k) = eom1 * dcosom1(k) + eom2 * dcosom2(k)*sss_ele_cut

       END DO
 !c! Radial stuff
       DO k = 1, 3
       END DO
 !c! Radial stuff
       DO k = 1, 3

@@ -27969,7 +28020,7 @@ C !!!!!!!! NIE CZYTANE !!!!!!!!!!!
                    - dQUADdR * pom&
                    - tuna(k) &
              + (eom12*(dc_norm(k,nres+j)-om12*dc_norm(k,nres+i))&
                    - dQUADdR * pom&
                    - tuna(k) &
              + (eom12*(dc_norm(k,nres+j)-om12*dc_norm(k,nres+i))&

-             + eom1*(erij(k)-om1*dc_norm(k,nres+i)))*dsci_inv
+             + eom1*(erij(k)-om1*dc_norm(k,nres+i)))*dsci_inv*sss_ele_cut

 
        pom = erhead(k)+facd2*(erhead(k)-erdxj*dC_norm(k,j+nres))
 !c! this acts on hydrophobic center of interaction
 
        pom = erhead(k)+facd2*(erhead(k)-erdxj*dC_norm(k,j+nres))
 !c! this acts on hydrophobic center of interaction

@@ -27984,7 +28035,7 @@ C !!!!!!!! NIE CZYTANE !!!!!!!!!!!
                    + dQUADdR * pom &
                    + tuna(k) &
              + (eom12*(dc_norm(k,nres+i)-om12*dc_norm(k,nres+j)) &
                    + dQUADdR * pom &
                    + tuna(k) &
              + (eom12*(dc_norm(k,nres+i)-om12*dc_norm(k,nres+j)) &

-             + eom2*(erij(k)-om2*dc_norm(k,nres+j)))*dscj_inv
+             + eom2*(erij(k)-om2*dc_norm(k,nres+j)))*dscj_inv*sss_ele_cut

 
 !c! this acts on Calpha
        gheadtail(k,3,1) = gheadtail(k,3,1)  &
 
 !c! this acts on Calpha
        gheadtail(k,3,1) = gheadtail(k,3,1)  &

@@ -28083,7 +28134,8 @@ C !!!!!!!! NIE CZYTANE !!!!!!!!!!!
        dFGBdOM2 = (((R1 * R1 * chi1 * om2) / (MomoFac1 * MomoFac1)) &
             * (2.0d0 - 0.5d0 * ee1) ) &
             / (2.0d0 * fgb1)
        dFGBdOM2 = (((R1 * R1 * chi1 * om2) / (MomoFac1 * MomoFac1)) &
             * (2.0d0 - 0.5d0 * ee1) ) &
             / (2.0d0 * fgb1)

-       dPOLdR1 = dPOLdFGB1 * dFGBdR1
+       dPOLdR1 = dPOLdFGB1 * dFGBdR1*sss_ele_cut+epol*sss_ele_grad
+        epol=epol*sss_ele_cut

 !c!       dPOLdR1 = 0.0d0
        dPOLdOM1 = 0.0d0
        dPOLdOM2 = dPOLdFGB1 * dFGBdOM2
 !c!       dPOLdR1 = 0.0d0
        dPOLdOM1 = 0.0d0
        dPOLdOM2 = dPOLdFGB1 * dFGBdOM2

@@ -28144,7 +28196,8 @@ C !!!!!!!! NIE CZYTANE !!!!!!!!!!!
        dFGBdOM1 = (((R2 * R2 * chi2 * om1) / (MomoFac2 * MomoFac2)) &
             * (2.0d0 - 0.5d0 * ee2) ) &
             / (2.0d0 * fgb2)
        dFGBdOM1 = (((R2 * R2 * chi2 * om1) / (MomoFac2 * MomoFac2)) &
             * (2.0d0 - 0.5d0 * ee2) ) &
             / (2.0d0 * fgb2)

-       dPOLdR2 = dPOLdFGB2 * dFGBdR2
+       dPOLdR2 = dPOLdFGB2 * dFGBdR2*sss_ele_cut+epol*sss_ele_grad
+       epol=epol*sss_ele_cut

 !c!       dPOLdR2 = 0.0d0
        dPOLdOM1 = dPOLdFGB2 * dFGBdOM1
 !c!       dPOLdOM1 = 0.0d0
 !c!       dPOLdR2 = 0.0d0
        dPOLdOM1 = dPOLdFGB2 * dFGBdOM1
 !c!       dPOLdOM1 = 0.0d0

@@ -28211,7 +28264,8 @@ C !!!!!!!! NIE CZYTANE !!!!!!!!!!!
        dFGBdOM1 = (((R2 * R2 * chi2 * om1) / (MomoFac2 * MomoFac2)) &
             * (2.0d0 - 0.5d0 * ee2) ) &
             / (2.0d0 * fgb2)
        dFGBdOM1 = (((R2 * R2 * chi2 * om1) / (MomoFac2 * MomoFac2)) &
             * (2.0d0 - 0.5d0 * ee2) ) &
             / (2.0d0 * fgb2)

-       dPOLdR2 = dPOLdFGB2 * dFGBdR2
+       dPOLdR2 = dPOLdFGB2 * dFGBdR2*sss_ele_cut+epol*sss_ele_grad
+       epol=epol*sss_ele_cut

 !c!       dPOLdR2 = 0.0d0
        dPOLdOM1 = dPOLdFGB2 * dFGBdOM1
 !c!       dPOLdOM1 = 0.0d0
 !c!       dPOLdR2 = 0.0d0
        dPOLdOM1 = dPOLdFGB2 * dFGBdOM1
 !c!       dPOLdOM1 = 0.0d0

@@ -28276,8 +28330,9 @@ C !!!!!!!! NIE CZYTANE !!!!!!!!!!!
        hawk     = w2 * Qi * Qi * (1.0d0 - sqom2)
        Ecl = sparrow / Rhead**2.0d0 &
          - hawk    / Rhead**4.0d0
        hawk     = w2 * Qi * Qi * (1.0d0 - sqom2)
        Ecl = sparrow / Rhead**2.0d0 &
          - hawk    / Rhead**4.0d0

-       dGCLdR  = - 2.0d0 * sparrow / Rhead**3.0d0 &
-             + 4.0d0 * hawk    / Rhead**5.0d0
+       dGCLdR  = (- 2.0d0 * sparrow / Rhead**3.0d0 &
+             + 4.0d0 * hawk    / Rhead**5.0d0)*sss_ele_cut+Ecl*sss_ele_grad
+       Ecl=Ecl*sss_ele_cut

 !c! dF/dom1
        dGCLdOM1 = (w1 * Qi) / (Rhead**2.0d0)
 !c! dF/dom2
 !c! dF/dom1
        dGCLdOM1 = (w1 * Qi) / (Rhead**2.0d0)
 !c! dF/dom2

@@ -28301,7 +28356,7 @@ C !!!!!!!! NIE CZYTANE !!!!!!!!!!!
        dFGBdOM2 = (((R1 * R1 * chi1 * om2) / (MomoFac1 * MomoFac1)) &
              * (2.0d0 - 0.5d0 * ee1) ) &
              / (2.0d0 * fgb1)
        dFGBdOM2 = (((R1 * R1 * chi1 * om2) / (MomoFac1 * MomoFac1)) &
              * (2.0d0 - 0.5d0 * ee1) ) &
              / (2.0d0 * fgb1)

-       dPOLdR1 = dPOLdFGB1 * dFGBdR1
+       dPOLdR1 = dPOLdFGB1 * dFGBdR1*sss_ele_cut+epol*sss_ele_grad

 !c!       dPOLdR1 = 0.0d0
        dPOLdOM1 = 0.0d0
        dPOLdOM2 = dPOLdFGB1 * dFGBdOM2
 !c!       dPOLdR1 = 0.0d0
        dPOLdOM1 = 0.0d0
        dPOLdOM2 = dPOLdFGB1 * dFGBdOM2

@@ -28313,7 +28368,8 @@ C !!!!!!!! NIE CZYTANE !!!!!!!!!!!
 !c! derivative of Elj is Glj
        dGLJdR = 4.0d0 * eps_head &
         * (((-12.0d0*pis**12.0d0)/(Rhead**13.0d0)) &
 !c! derivative of Elj is Glj
        dGLJdR = 4.0d0 * eps_head &
         * (((-12.0d0*pis**12.0d0)/(Rhead**13.0d0)) &

-        +  ((  6.0d0*pis**6.0d0) /(Rhead**7.0d0)))
+        +  ((  6.0d0*pis**6.0d0) /(Rhead**7.0d0)))*sss_ele_cut+elj*sss_ele_grad
+       Elj=Elj*sss_ele_cut

        DO k = 1, 3
       erhead(k) = Rhead_distance(k)/Rhead
       erhead_tail(k,1) = ((ctail(k,2)-chead(k,1))/R1)
        DO k = 1, 3
       erhead(k) = Rhead_distance(k)/Rhead
       erhead_tail(k,1) = ((ctail(k,2)-chead(k,1))/R1)

@@ -28358,6 +28414,126 @@ C !!!!!!!! NIE CZYTANE !!!!!!!!!!!
        END DO
        RETURN
       END SUBROUTINE eqd
        END DO
        RETURN
       END SUBROUTINE eqd

+
+      SUBROUTINE eqd_cat(Ecl,Elj,Epol)
+      use calc_data
+      use comm_momo
+       double precision  facd4, federmaus,ecl,elj,epol
+       alphapol1 = alphapolcat(itypi,itypj)
+       w1        = wqdipcat(1,itypi,itypj)
+       w2        = wqdipcat(2,itypi,itypj)
+       pis       = sig0headcat(itypi,itypj)
+       eps_head   = epsheadcat(itypi,itypj)
+!       eps_head=0.0d0
+!       w2=0.0d0
+!       alphapol1=0.0d0
+!c!-------------------------------------------------------------------
+!c! R1 - distance between head of ith side chain and tail of jth sidechain
+       R1 = 0.0d0
+       DO k = 1, 3
+!c! Calculate head-to-tail distances
+      R1=R1+(ctail(k,2)-chead(k,1))**2
+       END DO
+!c! Pitagoras
+       R1 = dsqrt(R1)
+
+!c!      R1     = dsqrt((Rtail**2)+((dtail(1,itypi,itypj)
+!c!     &        +dhead(1,1,itypi,itypj))**2))
+!c!      R2     = dsqrt((Rtail**2)+((dtail(2,itypi,itypj)
+!c!     &        +dhead(2,1,itypi,itypj))**2))
+
+!c!-------------------------------------------------------------------
+!c! ecl
+       sparrow  = w1 * Qi * om1
+       hawk     = w2 * Qi * Qi * (1.0d0 - sqom2)
+       Ecl = sparrow / Rhead**2.0d0 &
+         - hawk    / Rhead**4.0d0
+       dGCLdR  =sss_ele_cut*(-2.0d0 * sparrow / Rhead**3.0d0 &
+             + 4.0d0 * hawk    / Rhead**5.0d0)+sss_ele_grad*ECL
+       ECL=ECL*sss_ele_cut
+!c! dF/dom1
+       dGCLdOM1 = (w1 * Qi) / (Rhead**2.0d0)
+!c! dF/dom2
+       dGCLdOM2 = 0.0d0 !
+       
+!(2.0d0 * w2 * Qi * Qi * om2) / (Rhead ** 4.0d0)
+
+!c--------------------------------------------------------------------
+!c Polarization energy
+!c Epol
+       MomoFac1 = (1.0d0 - chi1 * sqom2)
+       RR1  = R1 * R1 / MomoFac1
+       ee1  = exp(-( RR1 / (4.0d0 * a12sq) ))
+       fgb1 = sqrt( RR1 + a12sq * ee1)
+       epol = 332.0d0 * eps_inout_fac * (( alphapol1 / fgb1 )**4.0d0)
+!c!       epol = 0.0d0
+!c!------------------------------------------------------------------
+!c! derivative of Epol is Gpol...
+       dPOLdFGB1 = -(1328.0d0 * eps_inout_fac * alphapol1 ** 4.0d0) &
+             / (fgb1 ** 5.0d0)
+       dFGBdR1 = ( (R1 / MomoFac1)  &
+           * ( 2.0d0 - (0.5d0 * ee1) ) ) &
+           / ( 2.0d0 * fgb1 )
+       dFGBdOM2 = 0.0d0 ! as om2 is 0
+! (((R1 * R1 * chi1 * om2) / (MomoFac1 * MomoFac1)) &
+!             * (2.0d0 - 0.5d0 * ee1) ) &
+!             / (2.0d0 * fgb1)
+       dPOLdR1 = dPOLdFGB1 * dFGBdR1*sss_ele_cut+epol*sss_ele_grad
+!c!       dPOLdR1 = 0.0d0
+       dPOLdOM1 = 0.0d0
+!       dPOLdOM2 = dPOLdFGB1 * dFGBdOM2
+       dPOLdOM2 = 0.0d0
+       epol=epol*sss_ele_cut
+!c!-------------------------------------------------------------------
+!c! Elj
+       pom = (pis / Rhead)**6.0d0
+       Elj = 4.0d0 * eps_head * pom * (pom-1.0d0)
+!c! derivative of Elj is Glj
+       dGLJdR = 4.0d0 * eps_head*sss_ele_cut &
+        * (((-12.0d0*pis**12.0d0)/(Rhead**13.0d0)) &
+        +  ((  6.0d0*pis**6.0d0) /(Rhead**7.0d0)))+Elj*sss_ele_grad
+       Elj=Elj*sss_ele_cut
+       DO k = 1, 3
+      erhead(k) = Rhead_distance(k)/Rhead
+      erhead_tail(k,1) = ((ctail(k,2)-chead(k,1))/R1)
+       END DO
+
+       erdxi = scalar( erhead(1), dC_norm(1,i+nres) )
+       bat = scalar( erhead_tail(1,1), dC_norm(1,i+nres) )
+       facd1 = d1 * vbld_inv(i+nres)
+
+       DO k = 1, 3
+      hawk = (erhead_tail(k,1) +  &
+      facd1 * (erhead_tail(k,1) - bat * dC_norm(k,i+nres)))
+
+      pom = erhead(k)+facd1*(erhead(k)-erdxi*dC_norm(k,i+nres))
+      gradpepcatx(k,i) = gradpepcatx(k,i)  &
+               - dGCLdR * pom&
+               - dPOLdR1 * hawk &
+               - dGLJdR * pom
+
+!      pom = erhead(k)+facd2*(erhead(k)-erdxj*dC_norm(k,j+nres))
+!      gradpepcatx(k,j) = gradpepcatx(k,j)    &
+!               + dGCLdR * pom  &
+!               + dPOLdR1 * (erhead_tail(k,1) &
+!       -facd4 * (erhead_tail(k,1) - federmaus * dC_norm(k,j+nres))) &
+!               + dGLJdR * pom
+
+
+      gradpepcat(k,i) = gradpepcat(k,i)          &
+               - dGCLdR * erhead(k)  &
+               - dPOLdR1 * erhead_tail(k,1) &
+               - dGLJdR * erhead(k)
+
+      gradpepcat(k,j) = gradpepcat(k,j)          &
+               + dGCLdR * erhead(k)  &
+               + dPOLdR1 * erhead_tail(k,1) &
+               + dGLJdR * erhead(k)
+
+       END DO
+       RETURN
+      END SUBROUTINE eqd_cat
+

       SUBROUTINE edq(Ecl,Elj,Epol)
 !       IMPLICIT NONE
        use comm_momo
       SUBROUTINE edq(Ecl,Elj,Epol)
 !       IMPLICIT NONE
        use comm_momo

@@ -28394,8 +28570,8 @@ C !!!!!!!! NIE CZYTANE !!!!!!!!!!!
 !c!-------------------------------------------------------------------
 !c! derivative of ecl is Gcl
 !c! dF/dr part
 !c!-------------------------------------------------------------------
 !c! derivative of ecl is Gcl
 !c! dF/dr part

-       dGCLdR  = - 2.0d0 * sparrow / Rhead**3.0d0 &
-             + 4.0d0 * hawk    / Rhead**5.0d0
+       dGCLdR  =sss_ele_cut*(- 2.0d0 * sparrow / Rhead**3.0d0 &
+             + 4.0d0 * hawk    / Rhead**5.0d0)+Ecl*sss_ele_grad

 !c! dF/dom1
        dGCLdOM1 = (w1 * Qj) / (Rhead**2.0d0)
 !c! dF/dom2
 !c! dF/dom1
        dGCLdOM1 = (w1 * Qj) / (Rhead**2.0d0)
 !c! dF/dom2

@@ -28416,7 +28592,8 @@ C !!!!!!!! NIE CZYTANE !!!!!!!!!!!
        dFGBdOM1 = (((R2 * R2 * chi2 * om1) / (MomoFac2 * MomoFac2)) &
             * (2.0d0 - 0.5d0 * ee2) ) &
             / (2.0d0 * fgb2)
        dFGBdOM1 = (((R2 * R2 * chi2 * om1) / (MomoFac2 * MomoFac2)) &
             * (2.0d0 - 0.5d0 * ee2) ) &
             / (2.0d0 * fgb2)

-       dPOLdR2 = dPOLdFGB2 * dFGBdR2
+       dPOLdR2 = dPOLdFGB2 * dFGBdR2*sss_ele_cut
+        epol=epol*sss_ele_cut

 !c!       dPOLdR2 = 0.0d0
        dPOLdOM1 = dPOLdFGB2 * dFGBdOM1
 !c!       dPOLdOM1 = 0.0d0
 !c!       dPOLdR2 = 0.0d0
        dPOLdOM1 = dPOLdFGB2 * dFGBdOM1
 !c!       dPOLdOM1 = 0.0d0

@@ -28428,7 +28605,8 @@ C !!!!!!!! NIE CZYTANE !!!!!!!!!!!
 !c! derivative of Elj is Glj
        dGLJdR = 4.0d0 * eps_head &
          * (((-12.0d0*pis**12.0d0)/(Rhead**13.0d0)) &
 !c! derivative of Elj is Glj
        dGLJdR = 4.0d0 * eps_head &
          * (((-12.0d0*pis**12.0d0)/(Rhead**13.0d0)) &

-         +  ((  6.0d0*pis**6.0d0) /(Rhead**7.0d0)))
+         +  ((  6.0d0*pis**6.0d0) /(Rhead**7.0d0)))*sss_ele_cut+Elj*sss_ele_grad
+        elj=elj*sss_ele_cut

 !c!-------------------------------------------------------------------
 !c! Return the results
 !c! (see comments in Eqq)
 !c!-------------------------------------------------------------------
 !c! Return the results
 !c! (see comments in Eqq)

@@ -28511,12 +28689,13 @@ C !!!!!!!! NIE CZYTANE !!!!!!!!!!!
 !c!-------------------------------------------------------------------
 !c! derivative of ecl is Gcl
 !c! dF/dr part
 !c!-------------------------------------------------------------------
 !c! derivative of ecl is Gcl
 !c! dF/dr part

-       dGCLdR  = - 2.0d0 * sparrow / Rhead**3.0d0 &
-             + 4.0d0 * hawk    / Rhead**5.0d0
+       dGCLdR  =( - 2.0d0 * sparrow / Rhead**3.0d0 &
+             + 4.0d0 * hawk    / Rhead**5.0d0)*sss_ele_cut+ECL*sss_ele_grad

 !c! dF/dom1
        dGCLdOM1 = (w1 * Qj) / (Rhead**2.0d0)
 !c! dF/dom2
        dGCLdOM2 = (2.0d0 * w2 * Qj * Qj * om2) / (Rhead ** 4.0d0)
 !c! dF/dom1
        dGCLdOM1 = (w1 * Qj) / (Rhead**2.0d0)
 !c! dF/dom2
        dGCLdOM2 = (2.0d0 * w2 * Qj * Qj * om2) / (Rhead ** 4.0d0)

+       ECL=ECL*sss_ele_cut

 !c--------------------------------------------------------------------
 !c--------------------------------------------------------------------
 !c Polarization energy
 !c--------------------------------------------------------------------
 !c--------------------------------------------------------------------
 !c Polarization energy

@@ -28534,11 +28713,12 @@ C !!!!!!!! NIE CZYTANE !!!!!!!!!!!
        dFGBdOM1 = (((R2 * R2 * chi2 * om1) / (MomoFac2 * MomoFac2)) &
             * (2.0d0 - 0.5d0 * ee2) ) &
             / (2.0d0 * fgb2)
        dFGBdOM1 = (((R2 * R2 * chi2 * om1) / (MomoFac2 * MomoFac2)) &
             * (2.0d0 - 0.5d0 * ee2) ) &
             / (2.0d0 * fgb2)

-       dPOLdR2 = dPOLdFGB2 * dFGBdR2
+       dPOLdR2 = dPOLdFGB2 * dFGBdR2*sss_ele_cut+epol*sss_ele_grad

 !c!       dPOLdR2 = 0.0d0
        dPOLdOM1 = dPOLdFGB2 * dFGBdOM1
 !c!       dPOLdOM1 = 0.0d0
        dPOLdOM2 = 0.0d0
 !c!       dPOLdR2 = 0.0d0
        dPOLdOM1 = dPOLdFGB2 * dFGBdOM1
 !c!       dPOLdOM1 = 0.0d0
        dPOLdOM2 = 0.0d0

+       epol=epol*sss_ele_cut

 !c!-------------------------------------------------------------------
 !c! Elj
        pom = (pis / Rhead)**6.0d0
 !c!-------------------------------------------------------------------
 !c! Elj
        pom = (pis / Rhead)**6.0d0

@@ -28546,7 +28726,9 @@ C !!!!!!!! NIE CZYTANE !!!!!!!!!!!
 !c! derivative of Elj is Glj
        dGLJdR = 4.0d0 * eps_head &
          * (((-12.0d0*pis**12.0d0)/(Rhead**13.0d0)) &
 !c! derivative of Elj is Glj
        dGLJdR = 4.0d0 * eps_head &
          * (((-12.0d0*pis**12.0d0)/(Rhead**13.0d0)) &

-         +  ((  6.0d0*pis**6.0d0) /(Rhead**7.0d0)))
+         +  ((  6.0d0*pis**6.0d0) /(Rhead**7.0d0)))*sss_ele_cut+&
+           Elj*sss_ele_grad
+       Elj=Elj*sss_ele_cut

 !c!-------------------------------------------------------------------
 
 !c! Return the results
 !c!-------------------------------------------------------------------
 
 !c! Return the results

@@ -28631,8 +28813,10 @@ C !!!!!!!! NIE CZYTANE !!!!!!!!!!!
 !c!-------------------------------------------------------------------
 !c! derivative of ecl is Gcl
 !c! dF/dr part
 !c!-------------------------------------------------------------------
 !c! derivative of ecl is Gcl
 !c! dF/dr part

-       dGCLdR  = - 2.0d0 * sparrow / Rhead**3.0d0 &
-             + 4.0d0 * hawk    / Rhead**5.0d0
+       dGCLdR  = (- 2.0d0 * sparrow / Rhead**3.0d0 &
+             + 4.0d0 * hawk    / Rhead**5.0d0)*sss_ele_cut+&
+             ECL*sss_ele_grad
+       ECL=ECL*sss_ele_cut

 !c! dF/dom1
        dGCLdOM1 = (w1 * Qj) / (Rhead**2.0d0)
 !c! dF/dom2
 !c! dF/dom1
        dGCLdOM1 = (w1 * Qj) / (Rhead**2.0d0)
 !c! dF/dom2

@@ -28654,7 +28838,8 @@ C !!!!!!!! NIE CZYTANE !!!!!!!!!!!
        dFGBdOM1 = (((R2 * R2 * chi2 * om1) / (MomoFac2 * MomoFac2)) &
             * (2.0d0 - 0.5d0 * ee2) ) &
             / (2.0d0 * fgb2)
        dFGBdOM1 = (((R2 * R2 * chi2 * om1) / (MomoFac2 * MomoFac2)) &
             * (2.0d0 - 0.5d0 * ee2) ) &
             / (2.0d0 * fgb2)

-       dPOLdR2 = dPOLdFGB2 * dFGBdR2
+       dPOLdR2 = dPOLdFGB2 * dFGBdR2*sss_ele_cut+epol*sss_ele_grad
+       epol=epol*sss_ele_grad

 !c!       dPOLdR2 = 0.0d0
        dPOLdOM1 = dPOLdFGB2 * dFGBdOM1
 !c!       dPOLdOM1 = 0.0d0
 !c!       dPOLdR2 = 0.0d0
        dPOLdOM1 = dPOLdFGB2 * dFGBdOM1
 !c!       dPOLdOM1 = 0.0d0

@@ -28664,9 +28849,10 @@ C !!!!!!!! NIE CZYTANE !!!!!!!!!!!
        pom = (pis / Rhead)**6.0d0
        Elj = 4.0d0 * eps_head * pom * (pom-1.0d0)
 !c! derivative of Elj is Glj
        pom = (pis / Rhead)**6.0d0
        Elj = 4.0d0 * eps_head * pom * (pom-1.0d0)
 !c! derivative of Elj is Glj

-       dGLJdR = 4.0d0 * eps_head &
+       dGLJdR = 4.0d0 * eps_head*sss_ele_cut &

          * (((-12.0d0*pis**12.0d0)/(Rhead**13.0d0)) &
          * (((-12.0d0*pis**12.0d0)/(Rhead**13.0d0)) &

-         +  ((  6.0d0*pis**6.0d0) /(Rhead**7.0d0)))
+         +  ((  6.0d0*pis**6.0d0) /(Rhead**7.0d0)))+Elj*sss_ele_grad
+       Elj=Elj*sss_ele_cut

 !c!-------------------------------------------------------------------
 
 !c! Return the results
 !c!-------------------------------------------------------------------
 
 !c! Return the results

@@ -28753,7 +28939,8 @@ C !!!!!!!! NIE CZYTANE !!!!!!!!!!!
        c1 = (-3.0d0 * w1 * fac) / (Rhead ** 4.0d0)
        c2 = (-6.0d0 * w2) / (Rhead ** 7.0d0) &
         * (4.0d0 + fac * fac - 3.0d0 * (sqom1 + sqom2))
        c1 = (-3.0d0 * w1 * fac) / (Rhead ** 4.0d0)
        c2 = (-6.0d0 * w2) / (Rhead ** 7.0d0) &
         * (4.0d0 + fac * fac - 3.0d0 * (sqom1 + sqom2))

-       dGCLdR = c1 - c2
+       dGCLdR = (c1 - c2)*sss_ele_cut+ECL*sss_ele_grad
+       ECL=ECL*sss_ele_cut

 !c! dECL/dom1
        c1 = (-3.0d0 * w1 * om2 ) / (Rhead**3.0d0)
        c2 = (-6.0d0 * w2) / (Rhead**6.0d0) &
 !c! dECL/dom1
        c1 = (-3.0d0 * w1 * om2 ) / (Rhead**3.0d0)
        c2 = (-6.0d0 * w2) / (Rhead**6.0d0) &

@@ -28790,6 +28977,132 @@ C !!!!!!!! NIE CZYTANE !!!!!!!!!!!
        END DO
        RETURN
       END SUBROUTINE edd
        END DO
        RETURN
       END SUBROUTINE edd

+      SUBROUTINE edd_cat(ECL)
+!       IMPLICIT NONE
+       use comm_momo
+      use calc_data
+
+       double precision ecl
+!c!       csig = sigiso(itypi,itypj)
+       w1 = wqdipcat(1,itypi,itypj)
+       w2 = wqdipcat(2,itypi,itypj)
+!       w2=0.0d0
+!c!-------------------------------------------------------------------
+!c! ECL
+!       print *,"om1",om1,om2,om12
+       fac = - 3.0d0 * om1 !after integer and simplify
+       c1 = (w1 / (Rhead**3.0d0)) * fac
+       c2 = (w2 / Rhead ** 6.0d0) &
+        * (4.0d0 + 6.0d0*sqom1 ) !after integration and simplification
+       ECL = c1 - c2
+!c! dervative of ECL is GCL...
+!c! dECL/dr
+       c1 = (-3.0d0 * w1 * fac) / (Rhead ** 4.0d0)
+       c2 = (-6.0d0 * w2) / (Rhead ** 7.0d0) &
+        * (4.0d0 + 6.0d0*sqom1)
+       dGCLdR = (c1 - c2)*sss_ele_cut+ECL*sss_ele_grad
+!c! dECL/dom1
+       c1 = (-3.0d0 * w1) / (Rhead**3.0d0)
+       c2 = (12.0d0 * w2*om1) / (Rhead**6.0d0) 
+       dGCLdOM1 = c1 - c2
+!c! dECL/dom2
+!       c1 = (-3.0d0 * w1 * om1 ) / (Rhead**3.0d0)
+       c1=0.0 ! this is because om2 is 0
+!       c2 = (-6.0d0 * w2) / (Rhead**6.0d0) &
+!        * ( om1 * om12 - 3.0d0 * sqom1 * om2 + om2 )
+       c2=0.0 !om is 0
+       dGCLdOM2 = c1 - c2
+!c! dECL/dom12
+!       c1 = w1 / (Rhead ** 3.0d0)
+       c1=0.0d0 ! this is because om12 is 0
+!       c2 = ( 2.0d0 * w2 * fac ) / Rhead ** 6.0d0
+       c2=0.0d0 !om12 is 0
+       dGCLdOM12 = c1 - c2
+!c!-------------------------------------------------------------------
+!c! Return the results
+!c! (see comments in Eqq)
+       DO k= 1, 3
+      erhead(k) = Rhead_distance(k)/Rhead
+       END DO
+       erdxi = scalar( erhead(1), dC_norm(1,i+nres) )
+       erdxj = scalar( erhead(1), dC_norm(1,j+nres) )
+       facd1 = d1 * vbld_inv(i+nres)
+       facd2 = d2 * vbld_inv(j+nres)
+       DO k = 1, 3
+
+      pom = erhead(k)+facd1*(erhead(k)-erdxi*dC_norm(k,i+nres))
+      gradpepcatx(k,i) = gradpepcatx(k,i)    - dGCLdR * pom
+!      pom = erhead(k)+facd2*(erhead(k)-erdxj*dC_norm(k,j+nres))
+!      gradpepcatx(k,j) = gradpepcatx(k,j)    + dGCLdR * pom
+
+      gradpepcat(k,i) = gradpepcat(k,i)    - dGCLdR * erhead(k)
+      gradpepcat(k,j) = gradpepcat(k,j)    + dGCLdR * erhead(k)
+       END DO
+       RETURN
+      END SUBROUTINE edd_cat
+      SUBROUTINE edd_cat_pep(ECL)
+!       IMPLICIT NONE
+       use comm_momo
+      use calc_data
+
+       double precision ecl
+!c!       csig = sigiso(itypi,itypj)
+       w1 = wqdipcat(1,itypi,itypj)
+       w2 = wqdipcat(2,itypi,itypj)
+!c!-------------------------------------------------------------------
+!c! ECL
+       fac = (om12 - 3.0d0 * om1 * om2)
+       c1 = (w1 / (Rhead**3.0d0)) * fac
+       c2 = (w2 / Rhead ** 6.0d0) &
+        * (4.0d0 + fac * fac -3.0d0 * (sqom1 + sqom2))
+       ECL = c1 - c2
+!c! dECL/dr
+       c1 = (-3.0d0 * w1 * fac) / (Rhead ** 4.0d0)
+       c2 = (-6.0d0 * w2) / (Rhead ** 7.0d0) &
+        * (4.0d0 + fac * fac - 3.0d0 * (sqom1 + sqom2))
+       dGCLdR = (c1 - c2)*sss_ele_cut+ECL*sss_ele_grad
+       ECL=ECL*sss_ele_cut
+!c! dECL/dom1
+       c1 = (-3.0d0 * w1 * om2 ) / (Rhead**3.0d0)
+       c2 = (-6.0d0 * w2) / (Rhead**6.0d0) &
+        * ( om2 * om12 - 3.0d0 * om1 * sqom2 + om1 )
+       dGCLdOM1 = c1 - c2
+!c! dECL/dom2
+       c1 = (-3.0d0 * w1 * om1 ) / (Rhead**3.0d0)
+       c2 = (-6.0d0 * w2) / (Rhead**6.0d0) &
+        * ( om1 * om12 - 3.0d0 * sqom1 * om2 + om2 )
+       dGCLdOM2 = c1 - c2
+       dGCLdOM2=0.0d0 ! this is because om2=0
+!c! dECL/dom12
+       c1 = w1 / (Rhead ** 3.0d0)
+       c2 = ( 2.0d0 * w2 * fac ) / Rhead ** 6.0d0
+       dGCLdOM12 = c1 - c2
+       dGCLdOM12=0.0d0 !this is because om12=0.0
+!c!-------------------------------------------------------------------
+!c! Return the results
+!c! (see comments in Eqq)
+       DO k= 1, 3
+      erhead(k) = Rhead_distance(k)/Rhead
+       END DO
+       erdxi = scalar( erhead(1), dC_norm(1,i) )
+       erdxj = scalar( erhead(1), dC_norm(1,j+nres) )
+       facd1 = d1 * vbld_inv(i)
+       facd2 = d2 * vbld_inv(j+nres)
+       DO k = 1, 3
+
+      pom = facd1*(erhead(k)-erdxi*dC_norm(k,i))
+      gradpepcat(k,i) = gradpepcat(k,i)    + dGCLdR * pom
+      gradpepcat(k,i+1) = gradpepcat(k,i+1) - dGCLdR * pom
+!      pom = erhead(k)+facd2*(erhead(k)-erdxj*dC_norm(k,j+nres))
+!      gradpepcatx(k,j) = gradpepcatx(k,j)    + dGCLdR * pom
+
+      gradpepcat(k,i) = gradpepcat(k,i)    - dGCLdR * erhead(k)*0.5d0
+      gradpepcat(k,i+1) = gradpepcat(k,i+1)- dGCLdR * erhead(k)*0.5d0
+      gradpepcat(k,j) = gradpepcat(k,j)    + dGCLdR * erhead(k)
+       END DO
+       RETURN
+      END SUBROUTINE edd_cat_pep
+

       SUBROUTINE elgrad_init(eheadtail,Egb,Ecl,Elj,Equad,Epol)
 !       IMPLICIT NONE
        use comm_momo
       SUBROUTINE elgrad_init(eheadtail,Egb,Ecl,Elj,Equad,Epol)
 !       IMPLICIT NONE
        use comm_momo

@@ -29851,8 +30164,12 @@ C !!!!!!!! NIE CZYTANE !!!!!!!!!!!
               if (itype(j,5).le.5) then
                  ilist_catscnorm=ilist_catscnorm+1
 ! this can be substituted by cantor and anti-cantor
               if (itype(j,5).le.5) then
                  ilist_catscnorm=ilist_catscnorm+1
 ! this can be substituted by cantor and anti-cantor

+!                 write(iout,*) "have contact",i,j,ilist_catscnorm

                  contlistcatscnormi(ilist_catscnorm)=i
                  contlistcatscnormj(ilist_catscnorm)=j
                  contlistcatscnormi(ilist_catscnorm)=i
                  contlistcatscnormj(ilist_catscnorm)=j

+!                 write(iout,*) "have contact2",i,j,ilist_catscnorm,&
+!               contlistcatscnormi(ilist_catscnorm),contlistcatscnormj(ilist_catscnorm)
+

               else
                  ilist_catsctran=ilist_catsctran+1
 ! this can be substituted by cantor and anti-cantor
               else
                  ilist_catsctran=ilist_catsctran+1
 ! this can be substituted by cantor and anti-cantor

@@ -29879,16 +30196,17 @@ C !!!!!!!! NIE CZYTANE !!!!!!!!!!!
       ilist_catscnorm,ilist_catpnorm,ilist_catscang
 
       do i=1,ilist_catsctran
       ilist_catscnorm,ilist_catpnorm,ilist_catscang
 
       do i=1,ilist_catsctran

-      write (iout,*) i,contlistcatsctrani(i),contlistcatsctranj(i)
+      write (iout,*) i,contlistcatsctrani(i),contlistcatsctranj(i),&
+      itype(j,contlistcatsctranj(i))

       enddo
       do i=1,ilist_catptran
       write (iout,*) i,contlistcatptrani(i),contlistcatsctranj(i)
       enddo
       do i=1,ilist_catscnorm
       enddo
       do i=1,ilist_catptran
       write (iout,*) i,contlistcatptrani(i),contlistcatsctranj(i)
       enddo
       do i=1,ilist_catscnorm

-      write (iout,*) i,contlistcatscnormi(i),contlistcatsctranj(i)
+      write (iout,*) i,contlistcatscnormi(i),contlistcatscnormj(i)

       enddo
       do i=1,ilist_catpnorm
       enddo
       do i=1,ilist_catpnorm

-      write (iout,*) i,contlistcatpnormi(i),contlistcatsctranj(i)
+      write (iout,*) i,contlistcatpnormi(i),contlistcatscnormj(i)

       enddo
       do i=1,ilist_catscang
       write (iout,*) i,contlistcatscangi(i),contlistcatscangi(i)
       enddo
       do i=1,ilist_catscang
       write (iout,*) i,contlistcatscangi(i),contlistcatscangi(i)

@@ -30216,7 +30534,7 @@ C !!!!!!!! NIE CZYTANE !!!!!!!!!!!
              i_ilist_catpnorm(0:nprocs),i_ilist_catsctran(0:nprocs),&
              i_ilist_catptran(0:nprocs),i_ilist_catscang(0:nprocs),&
              i_ilist_catscangf(0:nprocs),i_ilist_catscangt(0:nprocs)
              i_ilist_catpnorm(0:nprocs),i_ilist_catsctran(0:nprocs),&
              i_ilist_catptran(0:nprocs),i_ilist_catscang(0:nprocs),&
              i_ilist_catscangf(0:nprocs),i_ilist_catscangt(0:nprocs)

-            write(iout,*),"START make_catcat"
+!            write(iout,*),"START make_catcat"

             ilist_catpnorm=0
             ilist_catscnorm=0
             ilist_catptran=0
             ilist_catpnorm=0
             ilist_catscnorm=0
             ilist_catptran=0

@@ -30325,7 +30643,7 @@ C !!!!!!!! NIE CZYTANE !!!!!!!!!!!
       write (iout,*) i,newcontlistcatcatnormi(i),newcontlistcatcatnormj(i)
       enddo
 #endif
       write (iout,*) i,newcontlistcatcatnormi(i),newcontlistcatcatnormj(i)
       enddo
 #endif

-            write(iout,*),"END make_catcat"
+!            write(iout,*),"END make_catcat"

       return
       end subroutine make_cat_cat_list
 
       return
       end subroutine make_cat_cat_list
 

@@ -30412,6 +30730,7 @@ C !!!!!!!! NIE CZYTANE !!!!!!!!!!!
       boxx(1)=boxxsize
       boxx(2)=boxysize
       boxx(3)=boxzsize
       boxx(1)=boxxsize
       boxx(2)=boxysize
       boxx(3)=boxzsize

+      write(iout,*) "start ecattran",g_listcatsctran_start,g_listcatsctran_end

       do k=g_listcatsctran_start,g_listcatsctran_end
         i=newcontlistcatsctrani(k)
         j=newcontlistcatsctranj(k)
       do k=g_listcatsctran_start,g_listcatsctran_end
         i=newcontlistcatsctrani(k)
         j=newcontlistcatsctranj(k)

diff --git a/source/unres/io.F90 b/source/unres/io.F90
index 3f3c127..a147b46 100644 (file)
--- a/source/unres/io.F90
+++ b/source/unres/io.F90
@@ -2770,7 +2770,7 @@
 !c     &     itype(chain_border(1,i)+k).eq.itype(chain_border(1,j)+k))
           do k=0,chain_length(i)-1
 !c            k=k+1
 !c     &     itype(chain_border(1,i)+k).eq.itype(chain_border(1,j)+k))
           do k=0,chain_length(i)-1
 !c            k=k+1

-            mnum=molnum(k)
+            mnum=molnum(k+1)

             if (itype(chain_border(1,i)+k,mnum).ne.&
                itype(chain_border(1,j)+k,mnum)) exit
           enddo
             if (itype(chain_border(1,i)+k,mnum).ne.&
                itype(chain_border(1,j)+k,mnum)) exit
           enddo

diff --git a/source/unres/io_config.F90 b/source/unres/io_config.F90
index 48d2105..5efb730 100644 (file)
--- a/source/unres/io_config.F90
+++ b/source/unres/io_config.F90
@@ -880,7 +880,7 @@
              read(iion,*) msc(i,5),restok(i,5),ichargecat(i)
              print *,msc(i,5),restok(i,5)
             enddo
              read(iion,*) msc(i,5),restok(i,5),ichargecat(i)
              print *,msc(i,5),restok(i,5)
             enddo

-            ip(5)=0.2
+!            ip(5)=0.2

 !            isc(5)=0.2
             read (iion,*) ncatprotparm
             allocate(catprm(ncatprotparm,4))
 !            isc(5)=0.2
             read (iion,*) ncatprotparm
             allocate(catprm(ncatprotparm,4))

@@ -3431,11 +3431,12 @@
       !HERE THE MASS of MARTINI
       write(*,*) "before MARTINI PARAM"
       do i=1,ntyp_molec(4)
       !HERE THE MASS of MARTINI
       write(*,*) "before MARTINI PARAM"
       do i=1,ntyp_molec(4)

-       msc(i,4)=0.0d0
-       mp(4)=72.0d0
+       msc(i,4)=72.0d0
+       mp(4)=0.0d0

        isc(i,4)=0.d0
       enddo
       ip(4)=0.0
        isc(i,4)=0.d0
       enddo
       ip(4)=0.0

+      msc(ntyp_molec(4)+1,4)=0.1d0

       !relative dielectric constant = 15 for implicit screening
       k_coulomb_lip=332.0d0/15.0d0
       !kbond = 1250 kJ/(mol*nm*2)
       !relative dielectric constant = 15 for implicit screening
       k_coulomb_lip=332.0d0/15.0d0
       !kbond = 1250 kJ/(mol*nm*2)

@@ -3513,25 +3514,25 @@
 
 ! Ions by Aga
 
 
 ! Ions by Aga
 

-       allocate(alphapolcat(ntyp,ntyp),epsheadcat(ntyp,ntyp),sig0headcat(ntyp,ntyp))
-       allocate(alphapolcat2(ntyp,ntyp))
-       allocate(sigiso1cat(ntyp,ntyp),rborn1cat(ntyp,ntyp),rborn2cat(ntyp,ntyp),sigmap1cat(ntyp,ntyp))
-       allocate(sigmap2cat(ntyp,ntyp),sigiso2cat(ntyp,ntyp))
-       allocate(chis1cat(ntyp,ntyp),chis2cat(ntyp,ntyp),wquadcat(ntyp,ntyp),chipp1cat(ntyp,ntyp),chipp2cat(ntyp,ntyp))
-       allocate(epsintabcat(ntyp,ntyp))
-       allocate(dtailcat(2,ntyp,ntyp))
-       allocate(alphasurcat(4,ntyp,ntyp),alphisocat(4,ntyp,ntyp))
-       allocate(wqdipcat(2,ntyp,ntyp))
-       allocate(wstatecat(4,ntyp,ntyp))
-       allocate(dheadcat(2,2,ntyp,ntyp))
-       allocate(nstatecat(ntyp,ntyp))
-       allocate(debaykapcat(ntyp,ntyp))
-
-      if (.not.allocated(epscat)) allocate (epscat(0:ntyp1,0:ntyp1))
-      if (.not.allocated(sigmacat)) allocate(sigmacat(0:ntyp1,0:ntyp1))
+       allocate(alphapolcat(ntyp,-1:ntyp_molec(5)),epsheadcat(ntyp,-1:ntyp_molec(5)),sig0headcat(ntyp,-1:ntyp_molec(5)))
+       allocate(alphapolcat2(ntyp,-1:ntyp_molec(5)))
+       allocate(sigiso1cat(ntyp,-1:ntyp_molec(5)),rborn1cat(ntyp,-1:ntyp_molec(5)),rborn2cat(ntyp,-1:ntyp_molec(5)),sigmap1cat(ntyp,-1:ntyp_molec(5)))
+       allocate(sigmap2cat(ntyp,-1:ntyp_molec(5)),sigiso2cat(ntyp,-1:ntyp_molec(5)))
+       allocate(chis1cat(ntyp,-1:ntyp_molec(5)),chis2cat(ntyp,-1:ntyp_molec(5)),wquadcat(ntyp,-1:ntyp_molec(5)),chipp1cat(ntyp,-1:ntyp_molec(5)),chipp2cat(ntyp,-1:ntyp_molec(5)))
+       allocate(epsintabcat(ntyp,-1:ntyp_molec(5)))
+       allocate(dtailcat(2,ntyp,-1:ntyp_molec(5)))
+       allocate(alphasurcat(4,ntyp,-1:ntyp_molec(5)),alphisocat(4,ntyp,-1:ntyp_molec(5)))
+       allocate(wqdipcat(2,ntyp,-1:ntyp_molec(5)))
+       allocate(wstatecat(4,ntyp,-1:ntyp_molec(5)))
+       allocate(dheadcat(2,2,ntyp,-1:ntyp_molec(5)))
+       allocate(nstatecat(ntyp,-1:ntyp_molec(5)))
+       allocate(debaykapcat(ntyp,-1:ntyp_molec(5)))
+
+      if (.not.allocated(epscat)) allocate (epscat(0:ntyp1,-1:ntyp1))
+      if (.not.allocated(sigmacat)) allocate(sigmacat(0:ntyp1,-1:ntyp1))

 !      if (.not.allocated(chicat)) allocate(chicat(ntyp1,ntyp1)) !(ntyp,ntyp)
 !      if (.not.allocated(chicat)) allocate(chicat(ntyp1,ntyp1)) !(ntyp,ntyp)

-      if (.not.allocated(chi1cat)) allocate(chi1cat(ntyp1,ntyp1)) !(ntyp,ntyp)
-      if (.not.allocated(chi2cat)) allocate(chi2cat(ntyp1,ntyp1)) !(ntyp,ntyp)
+      if (.not.allocated(chi1cat)) allocate(chi1cat(ntyp1,-1:ntyp1)) !(ntyp,ntyp)
+      if (.not.allocated(chi2cat)) allocate(chi2cat(ntyp1,-1:ntyp1)) !(ntyp,ntyp)

 
 
             if (.not.allocated(ichargecat))&
 
 
             if (.not.allocated(ichargecat))&

@@ -3556,28 +3557,29 @@
            ! mp(5)=0.2
              pstok(5)=3.0
 !DIR$ NOUNROLL 
            ! mp(5)=0.2
              pstok(5)=3.0
 !DIR$ NOUNROLL 

-      do j=1,ntyp_molec(5)-1 ! this is without Zn will be modified for ALL tranistion metals
+      do j=-1,ntyp_molec(5)-1 ! this is without Zn will be modified for ALL tranistion metals
+       if (j.eq.0) cycle

        do i=1,ntyp
 !       do j=1,ntyp_molec(5)
 !        write (*,*) "Im in ALAB", i, " ", j
         read(iion,*) &
        epscat(i,j),sigmacat(i,j), &
 !       chicat(i,j),chicat(j,i),chippcat(i,j),chippcat(j,i), &
        do i=1,ntyp
 !       do j=1,ntyp_molec(5)
 !        write (*,*) "Im in ALAB", i, " ", j
         read(iion,*) &
        epscat(i,j),sigmacat(i,j), &
 !       chicat(i,j),chicat(j,i),chippcat(i,j),chippcat(j,i), &

-       chi1cat(i,j),chi2cat(i,j),chipp1cat(i,j),chipp2cat(i,j), &
+       chi1cat(i,j),chi2cat(i,j),chipp1cat(i,j),chipp2cat(i,j), & !6

 
 

-       (alphasurcat(k,i,j),k=1,4),sigmap1cat(i,j),sigmap2cat(i,j),&
+       (alphasurcat(k,i,j),k=1,4),sigmap1cat(i,j),sigmap2cat(i,j),&!12

 !       chiscat(i,j),chiscat(j,i), &
        chis1cat(i,j),chis2cat(i,j), &
 
 !       chiscat(i,j),chiscat(j,i), &
        chis1cat(i,j),chis2cat(i,j), &
 

-       nstatecat(i,j),(wstatecat(k,i,j),k=1,4), &                           !5 w tej lini - 1 integer pierwszy
-       dheadcat(1,1,i,j),dheadcat(1,2,i,j),dheadcat(2,1,i,j),dheadcat(2,2,i,j),&
+       nstatecat(i,j),(wstatecat(k,i,j),k=1,4), & !19                          !5 w tej lini - 1 integer pierwszy
+       dheadcat(1,1,i,j),dheadcat(1,2,i,j),dheadcat(2,1,i,j),dheadcat(2,2,i,j),&!23

        dtailcat(1,i,j),dtailcat(2,i,j), &
        dtailcat(1,i,j),dtailcat(2,i,j), &

-       epsheadcat(i,j),sig0headcat(i,j), &
+       epsheadcat(i,j),sig0headcat(i,j), &!27

 !wdipcat = w1 , w2
 !       rborncat(i,j),rborncat(j,i),&
        rborn1cat(i,j),rborn2cat(i,j),&
 !wdipcat = w1 , w2
 !       rborncat(i,j),rborncat(j,i),&
        rborn1cat(i,j),rborn2cat(i,j),&

-       (wqdipcat(k,i,j),k=1,2), &
-       alphapolcat(i,j),alphapolcat2(j,i), &
+       (wqdipcat(k,i,j),k=1,2), &!31
+       alphapolcat(i,j),alphapolcat2(j,i), &!33

        (alphisocat(k,i,j),k=1,4),sigiso1cat(i,j),sigiso2cat(i,j),epsintabcat(i,j),debaykapcat(i,j)
 
        if (chi1cat(i,j).gt.0.9) write (*,*) "WTF ANISO", i,j, chi1cat(i,j)
        (alphisocat(k,i,j),k=1,4),sigiso1cat(i,j),sigiso2cat(i,j),epsintabcat(i,j),debaykapcat(i,j)
 
        if (chi1cat(i,j).gt.0.9) write (*,*) "WTF ANISO", i,j, chi1cat(i,j)

@@ -3615,9 +3617,11 @@
 
        END DO
       END DO
 
        END DO
       END DO

-      allocate(aa_aq_cat(-ntyp:ntyp,ntyp),bb_aq_cat(-ntyp:ntyp,ntyp))
+      allocate(aa_aq_cat(-ntyp:ntyp,-1:ntyp_molec(5)),&
+               bb_aq_cat(-ntyp:ntyp,-1:ntyp_molec(5)))

       do i=1,ntyp
       do i=1,ntyp

-        do j=1,ntyp_molec(5)
+        do j=-1,ntyp_molec(5)
+          if (j.eq.0) cycle

           epsij=epscat(i,j)
           rrij=sigmacat(i,j)
           rrij=rrij**expon
           epsij=epscat(i,j)
           rrij=sigmacat(i,j)
           rrij=rrij**expon

diff --git a/source/unres/unres.F90 b/source/unres/unres.F90
index 804f228..c512cb1 100644 (file)
--- a/source/unres/unres.F90
+++ b/source/unres/unres.F90
@@ -126,7 +126,7 @@
         call exec_softreg
       else if (modecalc.eq.12) then
         call exec_MD
         call exec_softreg
       else if (modecalc.eq.12) then
         call exec_MD

-!        call exec_checkgrad
+        call exec_checkgrad

       else if (modecalc.eq.14) then
         call exec_MREMD
       else
       else if (modecalc.eq.14) then
         call exec_MREMD
       else