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+ 0.03590 4.57264 0.49749 0.00000 -0.04162 0.00000 0.06411 0.09670 0.10389 0.13065 2.97950 0.00000 0.09742 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_P1
+ 0.03671 4.60584 0.45793 0.00000 -0.05072 0.00000 0.06685 0.09703 0.10367 0.12797 2.97950 0.00000 0.09790 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_Nd
+ 0.03623 4.57493 0.43535 0.00000 0.00561 0.00000 0.06213 0.09644 0.10404 0.13437 2.97950 0.00000 0.09719 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_Nd
+ 0.03569 4.45940 0.54669 0.00000 -0.10213 0.00000 0.04409 0.09404 0.10588 0.14818 2.97950 0.00000 0.09579 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_Na
+ 0.03898 4.64447 0.42718 0.00000 -0.00071 0.00000 0.07593 0.09804 0.10288 0.12258 2.97950 0.00000 0.09791 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_N0
+ 0.03551 4.58262 0.38583 0.00000 0.00534 0.00000 0.06495 0.09677 0.10379 0.13158 2.97950 0.00000 0.09730 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_C5
+ 0.03536 4.50507 0.44258 0.00000 -0.02982 0.00000 0.04842 0.09471 0.10542 0.14258 2.97950 0.00000 0.09621 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_C4
+ 0.03482 4.59624 0.42881 0.00000 -0.04172 0.00000 0.06672 0.09702 0.10370 0.12712 2.97950 0.00000 0.09756 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_C3
+ 0.03681 4.65533 0.44456 0.00000 -0.02253 0.00000 0.07514 0.09795 0.10294 0.12269 2.97950 0.00000 0.09769 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_C2
+ 0.04321 4.73358 0.44819 0.00000 -0.00506 0.00000 0.08628 0.09921 0.10206 0.11353 2.97950 0.00000 0.09845 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_C1
+ 0.36710 3.84969 0.54979 0.00000 0.98351 0.00000 0.58680 0.37429 0.63109 1.61099 1.55307 0.00000 0.46217 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_Qda
+ 0.23140 4.06014 0.47236 0.00000 0.89014 0.00000 0.64463 0.04479 0.17839 0.80108 0.50594 0.00000 0.46212 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_Qd
+ 0.13094 4.15193 0.20993 0.00000 -0.76797 0.00000 5.02310 3.11567 4.50884 0.27630 2.94653 0.00000 0.48882 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_Qa
+ 3.76561 3.01980 0.39883 0.00000 0.36160 0.00000 2.78923 2.23171 0.35149 0.06104 2.83103 0.00000 0.17956 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_Q0
+ 1.09656 3.49638 0.31208 0.00000 0.28929 0.00000 0.09851 0.10064 0.10111 0.10248 2.99938 0.00000 0.46202 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_P5
+ 0.03468 4.33831 0.56652 0.00000 0.94376 0.00000 0.77659 0.03466 1.65121 0.59365 4.97643 0.00000 0.19873 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_P4
+ 0.76380 3.56659 0.46480 0.00000 0.85415 0.00000 13.85600 2.61212 13.82820 2.87473 2.06891 0.00000 0.53256 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_P3
+ 2.60699 3.06414 0.36473 0.00000 0.43138 0.00000 2.60066 1.47011 0.03466 0.03466 2.62323 0.00000 0.12463 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_P2
+ 1.20150 3.42579 0.35634 0.00000 0.33361 0.00000 0.10090 0.10091 0.10091 0.10091 3.00000 0.00000 0.46212 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_P1
+ 2.83805 3.44820 0.36170 0.00000 0.57370 0.00000 1.59165 0.83619 0.03466 0.03497 3.05900 0.00000 -0.09958 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_Nda
+ 1.46237 3.68646 0.26453 0.00000 0.35713 0.00000 0.58911 0.22341 0.03561 0.05854 3.21332 0.00000 0.06704 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_Nd
+ 1.16951 3.67617 0.34383 0.00000 0.24226 0.00000 0.10048 0.10086 0.10094 0.10125 2.99988 0.00000 0.46210 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_Na
+ 1.26795 3.52288 0.35380 0.00000 0.30502 0.00000 0.78422 0.32996 0.03466 0.07837 3.21788 0.00000 0.11625 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_N0
+ 2.32082 3.39143 0.35006 0.00000 0.43956 0.00000 1.57432 0.86513 0.03466 0.03495 2.89105 0.00000 0.13123 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_C5
+ 1.09870 3.48063 0.22198 0.00000 0.02694 0.00000 0.96914 0.59323 1.04447 0.40717 2.85401 0.00000 0.83228 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_C4
+ 2.02545 3.61929 0.14797 0.00000 0.24829 0.00000 1.08105 0.52046 0.03466 0.04082 3.11032 0.00000 0.09051 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_C3
+ 1.94249 4.02293 0.05661 0.00000 0.21757 0.00000 0.10056 0.10087 0.10094 0.10113 2.99989 0.00000 0.46211 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_C2
+ 3.15015 3.49435 0.24279 0.00000 0.26686 0.00000 1.93728 1.11986 0.03466 0.03541 2.98828 0.00000 0.12279 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_C1
+ 0.36710 3.84969 0.54979 0.00000 0.98351 0.00000 0.58680 0.37429 0.63109 1.61099 1.55307 0.00000 0.46217 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_Qda
+ 0.23140 4.06014 0.47236 0.00000 0.89014 0.00000 0.64463 0.04479 0.17839 0.80108 0.50594 0.00000 0.46212 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_Qd
+ 0.13094 4.15193 0.20993 0.00000 -0.76797 0.00000 5.02310 3.11567 4.50884 0.27630 2.94653 0.00000 0.48882 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_Qa
+ 3.76561 3.01980 0.39883 0.00000 0.36160 0.00000 2.78923 2.23171 0.35149 0.06104 2.83103 0.00000 0.17956 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_Q0
+ 1.09656 3.49638 0.31208 0.00000 0.28929 0.00000 0.09851 0.10064 0.10111 0.10248 2.99938 0.00000 0.46202 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_P5
+ 0.03468 4.33831 0.56652 0.00000 0.94376 0.00000 0.77659 0.03466 1.65121 0.59365 4.97643 0.00000 0.19873 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_P4
+ 0.76380 3.56659 0.46480 0.00000 0.85415 0.00000 13.85600 2.61212 13.82820 2.87473 2.06891 0.00000 0.53256 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_P3
+ 2.60699 3.06414 0.36473 0.00000 0.43138 0.00000 2.60066 1.47011 0.03466 0.03466 2.62323 0.00000 0.12463 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_P2
+ 1.20150 3.42579 0.35634 0.00000 0.33361 0.00000 0.10090 0.10091 0.10091 0.10091 3.00000 0.00000 0.46212 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_P1
+ 2.83805 3.44820 0.36170 0.00000 0.57370 0.00000 1.59165 0.83619 0.03466 0.03497 3.05900 0.00000 -0.09958 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_Nda
+ 1.46237 3.68646 0.26453 0.00000 0.35713 0.00000 0.58911 0.22341 0.03561 0.05854 3.21332 0.00000 0.06704 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_Nd
+ 1.16951 3.67617 0.34383 0.00000 0.24226 0.00000 0.10048 0.10086 0.10094 0.10125 2.99988 0.00000 0.46210 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_Na
+ 1.26795 3.52288 0.35380 0.00000 0.30502 0.00000 0.78422 0.32996 0.03466 0.07837 3.21788 0.00000 0.11625 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_N0
+ 2.32082 3.39143 0.35006 0.00000 0.43956 0.00000 1.57432 0.86513 0.03466 0.03495 2.89105 0.00000 0.13123 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_C5
+ 1.09870 3.48063 0.22198 0.00000 0.02694 0.00000 0.96914 0.59323 1.04447 0.40717 2.85401 0.00000 0.83228 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_C4
+ 2.02545 3.61929 0.14797 0.00000 0.24829 0.00000 1.08105 0.52046 0.03466 0.04082 3.11032 0.00000 0.09051 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_C3
+ 1.94249 4.02293 0.05661 0.00000 0.21757 0.00000 0.10056 0.10087 0.10094 0.10113 2.99989 0.00000 0.46211 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_C2
+ 3.15015 3.49435 0.24279 0.00000 0.26686 0.00000 1.93728 1.11986 0.03466 0.03541 2.98828 0.00000 0.12279 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_C1
! real(kind=8),dimension(:,:),allocatable :: gloc,gloc_x !(maxvar,2)
!----------------------------------------
real(kind=8),dimension(:,:),allocatable ::gradlipelec,gradlipbond,&
- gradlipang,gradliplj
+ gradlipang,gradliplj,gradpepmart, gradpepmartx
real(kind=8),dimension(:,:),allocatable :: gel_loc,gel_loc_long,&
gcorr3_turn,gcorr4_turn,gcorr6_turn,gradb,gradbx !(3,maxres)
! energies for protein nucleic acid interaction
real(kind=8) :: escbase,epepbase,escpho,epeppho
! energies for MARTINI
- real(kind=8) :: elipbond,elipang,elipelec,eliplj
+ real(kind=8) :: elipbond,elipang,elipelec,eliplj,elipidprot
#ifdef MPI
real(kind=8) :: weights_(n_ene) !,time_Bcast,time_Bcastw
weights_(49)=wpeppho
weights_(50)=wcatnucl
weights_(56)=wcat_tran
-
+ weights_(58)=wlip_prot
+ weights_(52)=wmartini
! wcatcat= weights(41)
! wcatprot=weights(42)
wscpho=weights(48)
wpeppho=weights(49)
wcatnucl=weights(50)
+ wmartini=weights(52)
wcat_tran=weights(56)
-
+ wlip_prot=weights(58)
! welpsb=weights(28)*fact(1)
!
! wcorr_nucl= weights(37)*fact(1)
! write (iout,*) "after make_SCp_inter_list"
if (mod(itime_mat,imatupdate).eq.0) call make_SCSC_inter_list
! write (iout,*) "after make_SCSC_inter_list"
-
+ if (nres_molec(4).gt.0) then
+ if (mod(itime_mat,imatupdate).eq.0) call make_lip_pep_list
+ endif
if (mod(itime_mat,imatupdate).eq.0) call make_pp_inter_list
if (nres_molec(5).gt.0) then
if (mod(itime_mat,imatupdate).eq.0) then
endif
call lipid_LJ(eliplj)
call lipid_elec(elipelec)
+ if (nres_molec(1).gt.0) then
+ call elip_prot(elipidprot)
+ else
+ elipidprot=0.0d0
+ endif
else
elipbond=0.0d0
elipang=0.0d0
energia(55)=elipelec
energia(56)=ecat_prottran
energia(57)=ecation_protang
+ energia(58)=elipidprot
! write(iout,*) elipelec,"elipelec"
! write(iout,*) elipang,"elipang"
! write(iout,*) eliplj,"eliplj"
ecation_nucl,ecat_prottran,ecation_protang
real(kind=8) :: escbase,epepbase,escpho,epeppho
integer :: i
- real(kind=8) :: elipbond,elipang,eliplj,elipelec
+ real(kind=8) :: elipbond,elipang,eliplj,elipelec,elipidprot
#ifdef MPI
integer :: ierr
real(kind=8) :: time00
elipelec=energia(55)
ecat_prottran=energia(56)
ecation_protang=energia(57)
+ elipidprot=energia(58)
! ecations_prot_amber=energia(50)
! energia(41)=ecation_prot
+wtor_d_nucl*etors_d_nucl+wcorr_nucl*ecorr_nucl+wcorr3_nucl*ecorr3_nucl&
+wcatprot*ecation_prot+wcatcat*ecationcation+wscbase*escbase&
+wpepbase*epepbase+wscpho*escpho+wpeppho*epeppho+wcatnucl*ecation_nucl&
- +elipbond+elipang+eliplj+elipelec+wcat_tran*ecat_prottran+ecation_protang&
+ +(elipbond+elipang+eliplj+elipelec)*wmartini&
+ +wcat_tran*ecat_prottran+ecation_protang&
+ +wlip_prot*elipidprot&
#ifdef WHAM_RUN
+0.0d0
#else
+wtor_d_nucl*etors_d_nucl+wcorr_nucl*ecorr_nucl+wcorr3_nucl*ecorr3_nucl&
+wcatprot*ecation_prot+wcatcat*ecationcation+wscbase*escbase&
+wpepbase*epepbase+wscpho*escpho+wpeppho*epeppho+wcatnucl*ecation_nucl&
- +elipbond+elipang+eliplj+elipelec+wcat_tran*ecat_prottran+ecation_protang&
+ +(elipbond+elipang+eliplj+elipelec)*wmartini&
+ +wcat_tran*ecat_prottran+ecation_protang&
+ +wlip_prot*elipidprot&
#ifdef WHAM_RUN
+0.0d0
#else
real(kind=8) :: ecation_prot,ecationcation,ecations_prot_amber,&
ecation_nucl,ecat_prottran,ecation_protang
real(kind=8) :: escbase,epepbase,escpho,epeppho
- real(kind=8) :: elipbond,elipang,eliplj,elipelec
+ real(kind=8) :: elipbond,elipang,eliplj,elipelec,elipidprot
etot=energia(0)
evdw=energia(1)
evdw2=energia(2)
ecat_prottran=energia(56)
ecation_protang=energia(57)
ehomology_constr=energia(51)
-
+ elipidprot=energia(58)
! ecations_prot_amber=energia(50)
#ifdef SPLITELE
write (iout,10) evdw,wsc,evdw2,wscp,ees,welec,evdw1,wvdwpp,&
ecationcation,wcatcat, &
escbase,wscbase,epepbase,wpepbase,escpho,wscpho,epeppho,wpeppho,&
ecation_nucl,wcatnucl,ehomology_constr,&
- elipbond,elipang,eliplj,elipelec,etot
+ elipbond,elipang,eliplj,elipelec,elipidprot,wlip_prot,etot
10 format (/'Virtual-chain energies:'// &
'EVDW= ',1pE16.6,' WEIGHT=',1pD16.6,' (SC-SC)'/ &
'EVDW2= ',1pE16.6,' WEIGHT=',1pD16.6,' (SC-p)'/ &
'ELIPANG=',1pE16.6,'(matrini angle energy)'/&
'ELIPLJ=',1pE16.6,'(matrini Lennard-Jones energy)'/&
'ELIPELEC=',1pE16.6,'(matrini electrostatic energy)'/&
+ 'ELIPPROT=',1pE16.6,' WEIGHT=',1pD16.6,'(lipid prot)'/ &
'ETOT= ',1pE16.6,' (total)')
#else
write (iout,10) evdw,wsc,evdw2,wscp,ees,welec,&
etors_d_nucl,wtor_d_nucl,ecorr_nucl,wcorr_nucl,&
ecorr3_nucl,wcorr3_nucl,ecation_prot,wcatprot,ecationcation,wcatcat, &
escbase,wscbase,epepbase,wpepbase,escpho,wscpho,epeppho,wpeppho,&
- ecation_nucl,wcatnucl,ehomology_constr,etot
+ ecation_nucl,wcatnucl,ehomology_constr,elipidprot,wlip_prot,etot
10 format (/'Virtual-chain energies:'// &
'EVDW= ',1pE16.6,' WEIGHT=',1pD16.6,' (SC-SC)'/ &
'EVDW2= ',1pE16.6,' WEIGHT=',1pD16.6,' (SC-p)'/ &
'ELIPANG=',1pE16.6,'(matrini angle energy)'/&
'ELIPLJ=',1pE16.6,'(matrini Lennard-Jones energy)'/&
'ELIPELEC=',1pE16.6,'(matrini electrostatic energy)'/&
+ 'ELIPPROT=',1pE16.6,' WEIGHT=',1pD16.6,'(lipid prot)'/ &
'ETOT= ',1pE16.6,' (total)')
#endif
return
wpepbase*gvdwc_pepbase(j,i)+&
wscpho*gvdwc_scpho(j,i)+ &
wpeppho*gvdwc_peppho(j,i)+wcatnucl*gradnuclcat(j,i)+ &
- gradlipbond(j,i)+gradlipang(j,i)+gradliplj(j,i)+gradlipelec(j,i)+&
- wcat_tran*gradcattranc(j,i)+gradcatangc(j,i)
+ wmartini*(gradlipbond(j,i)+gradlipang(j,i)+gradliplj(j,i)+gradlipelec(j,i))+&
+ wcat_tran*gradcattranc(j,i)+gradcatangc(j,i)+&
+ wlip_prot*gradpepmart(j,i)
+
wpepbase*gvdwc_pepbase(j,i)+&
wscpho*gvdwc_scpho(j,i)+&
wpeppho*gvdwc_peppho(j,i)+wcatnucl*gradnuclcat(j,i)+&
- gradlipbond(j,i)+gradlipang(j,i)+gradliplj(j,i)+gradlipelec(j,i)+&
- wcat_tran*gradcattranc(j,i)+gradcatangc(j,i)
+ wmartini*(gradlipbond(j,i)+gradlipang(j,i)+gradliplj(j,i)+gradlipelec(j,i))+&
+ wcat_tran*gradcattranc(j,i)+gradcatangc(j,i)+&
+ wlip_prot*gradpepmart(j,i)
+wscbase*gvdwx_scbase(j,i) &
+wpepbase*gvdwx_pepbase(j,i)&
+wscpho*gvdwx_scpho(j,i)+wcatnucl*gradnuclcatx(j,i)&
- +wcat_tran*gradcattranx(j,i)+gradcatangx(j,i)
+ +wcat_tran*gradcattranx(j,i)+gradcatangx(j,i)&
+ +wlip_prot*gradpepmartx(j,i)
+
! if (i.eq.3) print *,"tu?", wscpho,gvdwx_scpho(j,i)
enddo
! call intcartderiv
! call checkintcartgrad
call zerograd
- aincr=1.0D-5
+ aincr=graddelta
write(iout,*) 'Calling CHECK_ECARTINT.,kupa'
nf=0
icall=0
#endif
! print *, "before set matrices"
call set_matrices
-! print *,"after set martices"
+! print *,"after set catices"
#ifdef TIMING
time_mat=time_mat+MPI_Wtime()-time01
#endif
gradcattranx(j,i)=0.0d0
gradcatangx(j,i)=0.0d0
gradcatangc(j,i)=0.0d0
+ gradpepmart(j,i)=0.0d0
+ gradpepmartx(j,i)=0.0d0
duscdiff(j,i)=0.0d0
duscdiffx(j,i)=0.0d0
enddo
allocate(gvdwpp_nucl(3,-1:nres))
allocate(gradpepcat(3,-1:nres))
allocate(gradpepcatx(3,-1:nres))
+ allocate(gradpepmart(3,-1:nres))
+ allocate(gradpepmartx(3,-1:nres))
allocate(gradcatcat(3,-1:nres))
allocate(gradnuclcat(3,-1:nres))
allocate(gradnuclcatx(3,-1:nres))
allocate(newcontlistppj(300*nres))
allocate(newcontlistscpj(350*nres))
allocate(newcontlistj(300*nres))
+ allocate(newcontlistmartpi(300*nres))
+ allocate(newcontlistmartpj(300*nres))
+ allocate(newcontlistmartsci(300*nres))
+ allocate(newcontlistmartscj(300*nres))
+
allocate(newcontlistcatsctrani(300*nres))
allocate(newcontlistcatsctranj(300*nres))
allocate(newcontlistcatptrani(300*nres))
allocate(newcontlistcatpnormj(300*nres))
allocate(newcontlistcatcatnormi(900*nres))
allocate(newcontlistcatcatnormj(900*nres))
-
+
allocate(newcontlistcatscangi(300*nres))
allocate(newcontlistcatscangj(300*nres))
allocate(newcontlistcatscangfi(300*nres))
xj=boxshift(xj-xi,boxxsize)
yj=boxshift(yj-yi,boxysize)
zj=boxshift(zj-zi,boxzsize)
+ Rreal(1)=xj
+ Rreal(2)=yj
+ Rreal(3)=zj
dxj = dc_norm( 1, nres+j )
dyj = dc_norm( 2, nres+j )
dzj = dc_norm( 3, nres+j )
rij = dsqrt(rrij)
sss_ele_cut=sscale_ele(1.0d0/(rij))
sss_ele_grad=sscagrad_ele(1.0d0/(rij))
+! sss_ele_cut=1.0d0
+! sss_ele_grad=0.0d0
! print *,sss_ele_cut,sss_ele_grad,&
! 1.0d0/(rij),r_cut_ele,rlamb_ele
if (sss_ele_cut.le.0.0) cycle
sigder = fac * sigder
! fac = rij * fac
! Calculate distance derivative
- 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
+ gg(1) = fac*sss_ele_cut
+ gg(2) = fac*sss_ele_cut
+ gg(3) = fac*sss_ele_cut
! if (b2.gt.0.0) then
fac = chis1 * sqom1 + chis2 * sqom2 &
- 2.0d0 * chis12 * om1 * om2 * om12
dtop = b1cav * ((Lambf / (2.0d0 * eagle)) + (b2cav * Lambf))
dbot = 12.0d0 * b4cav * bat * Lambf
- dFdR = ((dtop * bot - top * dbot) / botsq) * sparrow*sss_ele_cut&
- +Fcav*sss_ele_grad
- Fcav=Fcav*sss
+ dFdR = ((dtop * bot - top * dbot) / botsq) * sparrow*sss_ele_cut
dtop = b1cav * ((Chif / (2.0d0 * eagle)) + (b2cav * Chif))
dbot = 12.0d0 * b4cav * bat * Chif
eagle = Lambf * pom
!c! write (*,*) "Gvdwc(",k,",",j,")=", gvdwc(k,j)
pom = ertail(k)-facd1*(ertail(k)-erdxi*dC_norm(k,i+nres))
gvdwx(k,i) = gvdwx(k,i) &
- - (( dFdR + gg(k) ) * pom)
+ - (( dFdR + gg(k) ) * pom)&
+ -sss_ele_grad*Rreal(k)*rij*(Fcav+evdwij)
!c! & - ( dFdR * pom )
pom = ertail(k)-facd2*(ertail(k)-erdxj*dC_norm(k,j+nres))
gvdwx(k,j) = gvdwx(k,j) &
- + (( dFdR + gg(k) ) * pom)
+ + (( dFdR + gg(k) ) * pom) &
+ +sss_ele_grad*Rreal(k)*rij*(Fcav+evdwij)
+
!c! & + ( dFdR * pom )
gvdwc(k,i) = gvdwc(k,i) &
- - (( dFdR + gg(k) ) * ertail(k))
+ - (( dFdR + gg(k) ) * ertail(k)) &
+ -sss_ele_grad*Rreal(k)*rij*(Fcav+evdwij)
+
!c! & - ( dFdR * ertail(k))
gvdwc(k,j) = gvdwc(k,j) &
- + (( dFdR + gg(k) ) * ertail(k))
+ + (( dFdR + gg(k) ) * ertail(k)) &
+ +sss_ele_grad*Rreal(k)*rij*(Fcav+evdwij)
+
!c! & + ( dFdR * ertail(k))
gg(k) = 0.0d0
! write (*,*) "Gvdwc(",k,",",i,")=", gvdwc(k,i)
! write (*,*) "Gvdwc(",k,",",j,")=", gvdwc(k,j)
END DO
-
+
!c! Compute head-head and head-tail energies for each state
! endif
! isel=0
+! if (isel.eq.2) isel=0
+! if (isel.eq.3) isel=0
+! if (iabs(Qj).eq.1) isel=0
+! nstate(itypi,itypj)=1
IF (isel.eq.0) THEN
!c! No charges - do nothing
eheadtail = 0.0d0
CALL energy_quad(istate,eheadtail,Ecl,Egb,Epol,Fisocav,Elj,Equad)
END IF
END IF ! this endif ends the "catch the gly-gly" at the beggining of Fcav
- evdw = evdw + Fcav + eheadtail
+ evdw = evdw + Fcav*sss_ele_cut + eheadtail*sss_ele_cut
IF (energy_dec) write (iout,'(2(1x,a3,i3),3f6.2,10f16.7)') &
restyp(itype(i,1),1),i,restyp(itype(j,1),1),j,&
use calc_data
use comm_momo
real (kind=8) :: facd3, facd4, federmaus, adler,&
- Ecl,Egb,Epol,Fisocav,Elj,Fgb,debkap
+ Ecl,Egb,Epol,Fisocav,Elj,Fgb,debkap,sgrad
! integer :: k
!c! Epol and Gpol analytical parameters
alphapol1 = alphapol(itypi,itypj)
!c! Coulomb electrostatic interaction
Ecl = (332.0d0 * Qij) / Rhead
!c! derivative of Ecl is Gcl...
- dGCLdR = (-332.0d0 * Qij ) / Rhead_sq*sss_ele_cut+ECL*sss_ele_grad
+ dGCLdR = (-332.0d0 * Qij ) / Rhead_sq*sss_ele_cut
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)
-(332.0d0 * Qij *&
(dexp(-debkap*Fgb)*debkap/eps_out))/ Fgb
dFGBdR = ( Rhead * ( 2.0d0 - (0.5d0 * ee0) ) )/ ( 2.0d0 * Fgb )
- dGGBdR = dGGBdFGB * dFGBdR*sss_ele_cut+Egb*sss_ele_grad
- Egb=Egb*sss_ele_cut
+ dGGBdR = dGGBdFGB * dFGBdR*sss_ele_cut
!c!-------------------------------------------------------------------
!c! Fisocav - isotropic cavity creation term
!c! or "how much energy it costs to put charged head in water"
!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
!c!-------------------------------------------------------------------
!c! Epol
!c! Polarization energy - charged heads polarize hydrophobic "neck"
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)))*sss_ele_cut+&
- (ELJ+epol)*sss_ele_grad
- epol=epol*sss_ele_cut
- Elj=Elj*sss_ele_cut
+ + (( 6.0d0*pis**6.0d0) /(Rhead**7.0d0)))*sss_ele_cut
!c!-------------------------------------------------------------------
!c! Return the results
!c! These things do the dRdX derivatives, that is
facd1 * (erhead_tail(k,1) - bat * dC_norm(k,i+nres)))
condor = (erhead_tail(k,2) + &
facd2 * (erhead_tail(k,2) - eagle * dC_norm(k,j+nres)))
-
+ sgrad=(Ecl+Egb+Epol+Fisocav+Elj)*sss_ele_grad*rreal(k)*rij
pom = erhead(k)+facd1*(erhead(k)-erdxi*dC_norm(k,i+nres))
gvdwx(k,i) = gvdwx(k,i) &
- dGCLdR * pom&
- dPOLdR1 * hawk&
- dPOLdR2 * (erhead_tail(k,2)&
-facd3 * (erhead_tail(k,2) - adler * dC_norm(k,i+nres)))&
- - dGLJdR * pom
+ - dGLJdR * pom-sgrad
pom = erhead(k)+facd2*(erhead(k)-erdxj*dC_norm(k,j+nres))
gvdwx(k,j) = gvdwx(k,j)+ dGCLdR * pom&
+ dGGBdR * pom+ dGCVdR * pom&
+ dPOLdR1 * (erhead_tail(k,1)&
-facd4 * (erhead_tail(k,1) - federmaus * dC_norm(k,j+nres)))&
- + dPOLdR2 * condor + dGLJdR * pom
+ + dPOLdR2 * condor + dGLJdR * pom+sgrad
gvdwc(k,i) = gvdwc(k,i) &
- dGCLdR * erhead(k)&
- dGCVdR * erhead(k)&
- dPOLdR1 * erhead_tail(k,1)&
- dPOLdR2 * erhead_tail(k,2)&
- - dGLJdR * erhead(k)
+ - dGLJdR * erhead(k)-sgrad
gvdwc(k,j) = gvdwc(k,j) &
+ dGCLdR * erhead(k) &
+ dGCVdR * erhead(k) &
+ dPOLdR1 * erhead_tail(k,1) &
+ dPOLdR2 * erhead_tail(k,2)&
- + dGLJdR * erhead(k)
+ + dGLJdR * erhead(k)+sgrad
END DO
RETURN
double precision dcosom1(3),dcosom2(3)
!c! used in Epol derivatives
double precision facd3, facd4
- double precision federmaus, adler
+ double precision federmaus, adler,sgrad
integer istate,ii,jj
real (kind=8) :: Fgb
! print *,"CALLING EQUAD"
!c! Ecl = 0.0d0
!c! write (*,*) "Ecl = ", Ecl
!c! derivative of Ecl is Gcl...
- dGCLdR = (-332.0d0 * Qij ) / (Rhead_sq * eps_in)*sss_ele_cut+ECL*sss_ele_grad
- ECL=ecl*sss_ele_cut
+ dGCLdR = (-332.0d0 * Qij ) / (Rhead_sq * eps_in)
!c! dGCLdR = 0.0d0
dGCLdOM1 = 0.0d0
dGCLdOM2 = 0.0d0
dGGBdFGB = -(-332.0d0 * Qij * eps_inout_fac) / (Fgb * Fgb)
dFGBdR = ( Rhead * ( 2.0d0 - (0.5d0 * ee0) ) )&
/ ( 2.0d0 * Fgb )
- dGGBdR = dGGBdFGB * dFGBdR*sss_ele_cut+Egb*sss_ele_grad
- Egb=Egb*sss_ele_cut
+ dGGBdR = dGGBdFGB * dFGBdR
!c! dGGBdR = 0.0d0
!c!-------------------------------------------------------------------
!c! Fisocav - isotropic cavity creation term
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*sss_ele_cut+FisoCav*sss_ele_grad
- FisoCav=FisoCav*sss_ele_cut
+ dGCVdR = ((dtop * bot - top * dbot) / botsq) * csig
!c! dGCVdR = 0.0d0
!c!-------------------------------------------------------------------
dFGBdOM1 = (((R2 * R2 * chi2 * om1) / (MomoFac2 * MomoFac2)) &
* ( 2.0d0 - 0.5d0 * ee2) ) &
/ ( 2.0d0 * fgb2 )
- dPOLdR1 = dPOLdFGB1 * dFGBdR1*sss_ele_cut
+ dPOLdR1 = dPOLdFGB1 * dFGBdR1
!c! dPOLdR1 = 0.0d0
- dPOLdR2 = dPOLdFGB2 * dFGBdR2*sss_ele_cut
+ dPOLdR2 = dPOLdFGB2 * dFGBdR2
!c! dPOLdR2 = 0.0d0
dPOLdOM1 = dPOLdFGB2 * dFGBdOM1
!c! dPOLdOM1 = 0.0d0
!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)))*sss_ele_cut+&
- (epol+Elj)*sss_ele_grad
- Elj=Elj*sss_ele_cut
- epol=epol*sss_ele_cut
+ + (( 6.0d0*pis**6.0d0) /(Rhead**7.0d0)))
!c! dGLJdR = 0.0d0
!c!-------------------------------------------------------------------
!c! Equad
Equad = fac * Beta1
!c! Equad = 0.0d0
!c! derivative of Equad...
- dQUADdR = ((2.5d0 * Wqd * Beta1) / (Fgb**6.0d0)) * dFGBdR*sss_ele_cut&
- + Equad*sss_ele_grad
- Equad=Equad*sss_ele_cut
+ dQUADdR = ((2.5d0 * Wqd * Beta1) / (Fgb**6.0d0)) * dFGBdR
!c! dQUADdR = 0.0d0
dQUADdOM1 = fac* (-75.0d0*om1 + 315.0d0*om1*sqom2 - 45.0d0*om2*om12)
!c! dQUADdOM1 = 0.0d0
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)*sss_ele_cut
+ tuna(k) = eom1 * dcosom1(k) + eom2 * dcosom2(k)
END DO
!c! Radial stuff
DO k = 1, 3
pom = erhead(k)+facd1*(erhead(k)-erdxi*dC_norm(k,i+nres))
!c! this acts on hydrophobic center of interaction
+! sgrad=sss_ele_grad*(Ecl+Egb+FisoCav+epol+Elj)*rij*rreal(k)
gheadtail(k,1,1) = gheadtail(k,1,1) &
- dGCLdR * pom &
- dGGBdR * pom &
DO l = 1, 4
gheadtail(k,l,2) = gheadtail(k,l,2) / eheadtail
END DO
- gvdwx(k,i) = gvdwx(k,i) + gheadtail(k,1,2)
- gvdwx(k,j) = gvdwx(k,j) + gheadtail(k,2,2)
- gvdwc(k,i) = gvdwc(k,i) + gheadtail(k,3,2)
- gvdwc(k,j) = gvdwc(k,j) + gheadtail(k,4,2)
+ gvdwx(k,i) = gvdwx(k,i) + gheadtail(k,1,2)*sss_ele_cut
+ gvdwx(k,j) = gvdwx(k,j) + gheadtail(k,2,2)*sss_ele_cut
+ gvdwc(k,i) = gvdwc(k,i) + gheadtail(k,3,2)*sss_ele_cut
+ gvdwc(k,j) = gvdwc(k,j) + gheadtail(k,4,2)*sss_ele_cut
DO l = 1, 4
gheadtail(k,l,1) = 0.0d0
gheadtail(k,l,2) = 0.0d0
END DO
END DO
eheadtail = (-dlog(eheadtail)) / betaT
+ do k=1,3
+ gvdwx(k,i) = gvdwx(k,i) - eheadtail*sss_ele_grad*rreal(k)*rij
+ gvdwx(k,j) = gvdwx(k,j) + eheadtail*sss_ele_grad*rreal(k)*rij
+ gvdwc(k,i) = gvdwc(k,i) - eheadtail*sss_ele_grad*rreal(k)*rij
+ gvdwc(k,j) = gvdwc(k,j) + eheadtail*sss_ele_grad*rreal(k)*rij
+ enddo
dPOLdOM1 = 0.0d0
dPOLdOM2 = 0.0d0
dQUADdOM1 = 0.0d0
dFGBdOM2 = (((R1 * R1 * chi1 * om2) / (MomoFac1 * MomoFac1)) &
* (2.0d0 - 0.5d0 * ee1) ) &
/ (2.0d0 * fgb1)
- dPOLdR1 = dPOLdFGB1 * dFGBdR1*sss_ele_cut+epol*sss_ele_grad
- epol=epol*sss_ele_cut
+ dPOLdR1 = dPOLdFGB1 * dFGBdR1*sss_ele_cut
+! epol=epol*sss_ele_cut
!c! dPOLdR1 = 0.0d0
dPOLdOM1 = 0.0d0
dPOLdOM2 = dPOLdFGB1 * dFGBdOM2
facd1 * (erhead_tail(k,1) - bat * dC_norm(k,i+nres)))
gvdwx(k,i) = gvdwx(k,i) &
- - dPOLdR1 * hawk
+ - dPOLdR1 * hawk-epol*sss_ele_grad*rreal(k)*rij
gvdwx(k,j) = gvdwx(k,j) &
+ dPOLdR1 * (erhead_tail(k,1) &
- -facd4 * (erhead_tail(k,1) - federmaus * dC_norm(k,j+nres)))
+ -facd4 * (erhead_tail(k,1) - federmaus * dC_norm(k,j+nres)))&
+ +epol*sss_ele_grad*rreal(k)*rij
- gvdwc(k,i) = gvdwc(k,i) - dPOLdR1 * erhead_tail(k,1)
- gvdwc(k,j) = gvdwc(k,j) + dPOLdR1 * erhead_tail(k,1)
+ gvdwc(k,i) = gvdwc(k,i) - dPOLdR1 * erhead_tail(k,1)&
+ -epol*sss_ele_grad*rreal(k)*rij
+ gvdwc(k,j) = gvdwc(k,j) + dPOLdR1 * erhead_tail(k,1)&
+ +epol*sss_ele_grad*rreal(k)*rij
END DO
RETURN
dFGBdOM1 = (((R2 * R2 * chi2 * om1) / (MomoFac2 * MomoFac2)) &
* (2.0d0 - 0.5d0 * ee2) ) &
/ (2.0d0 * fgb2)
- dPOLdR2 = dPOLdFGB2 * dFGBdR2*sss_ele_cut+epol*sss_ele_grad
- epol=epol*sss_ele_cut
+ dPOLdR2 = dPOLdFGB2 * dFGBdR2*sss_ele_cut
+! epol=epol*sss_ele_cut
!c! dPOLdR2 = 0.0d0
dPOLdOM1 = dPOLdFGB2 * dFGBdOM1
!c! dPOLdOM1 = 0.0d0
gvdwx(k,i) = gvdwx(k,i) &
- dPOLdR2 * (erhead_tail(k,2) &
- -facd3 * (erhead_tail(k,2) - adler * dC_norm(k,i+nres)))
+ -facd3 * (erhead_tail(k,2) - adler * dC_norm(k,i+nres)))&
+ -epol*sss_ele_grad*rreal(k)*rij
gvdwx(k,j) = gvdwx(k,j) &
- + dPOLdR2 * condor
+ + dPOLdR2 * condor+epol*sss_ele_grad*rreal(k)*rij
+
gvdwc(k,i) = gvdwc(k,i) &
- - dPOLdR2 * erhead_tail(k,2)
+ - dPOLdR2 * erhead_tail(k,2)-epol*sss_ele_grad*rreal(k)*rij
+
gvdwc(k,j) = gvdwc(k,j) &
- + dPOLdR2 * erhead_tail(k,2)
+ + dPOLdR2 * erhead_tail(k,2)+epol*sss_ele_grad*rreal(k)*rij
+
END DO
RETURN
SUBROUTINE eqd(Ecl,Elj,Epol)
use calc_data
use comm_momo
- double precision facd4, federmaus,ecl,elj,epol
+ double precision facd4, federmaus,ecl,elj,epol,sgrad
alphapol1 = alphapol(itypi,itypj)
w1 = wqdip(1,itypi,itypj)
w2 = wqdip(2,itypi,itypj)
Ecl = sparrow / Rhead**2.0d0 &
- hawk / Rhead**4.0d0
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
+ + 4.0d0 * hawk / Rhead**5.0d0)*sss_ele_cut
!c! dF/dom1
dGCLdOM1 = (w1 * Qi) / (Rhead**2.0d0)
!c! dF/dom2
dFGBdOM2 = (((R1 * R1 * chi1 * om2) / (MomoFac1 * MomoFac1)) &
* (2.0d0 - 0.5d0 * ee1) ) &
/ (2.0d0 * fgb1)
- dPOLdR1 = dPOLdFGB1 * dFGBdR1*sss_ele_cut+epol*sss_ele_grad
+ dPOLdR1 = dPOLdFGB1 * dFGBdR1*sss_ele_cut
!c! dPOLdR1 = 0.0d0
dPOLdOM1 = 0.0d0
dPOLdOM2 = dPOLdFGB1 * dFGBdOM2
!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)))*sss_ele_cut+elj*sss_ele_grad
- Elj=Elj*sss_ele_cut
+ + (( 6.0d0*pis**6.0d0) /(Rhead**7.0d0)))*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
hawk = (erhead_tail(k,1) + &
facd1 * (erhead_tail(k,1) - bat * dC_norm(k,i+nres)))
-
+ sgrad=(epol+elj+ecl)*sss_ele_grad*rreal(k)*rij
pom = erhead(k)+facd1*(erhead(k)-erdxi*dC_norm(k,i+nres))
gvdwx(k,i) = gvdwx(k,i) &
- dGCLdR * pom&
- dPOLdR1 * hawk &
- - dGLJdR * pom
-
+ - dGLJdR * pom &
+ -sgrad
+
pom = erhead(k)+facd2*(erhead(k)-erdxj*dC_norm(k,j+nres))
gvdwx(k,j) = gvdwx(k,j) &
+ dGCLdR * pom &
+ dPOLdR1 * (erhead_tail(k,1) &
-facd4 * (erhead_tail(k,1) - federmaus * dC_norm(k,j+nres))) &
- + dGLJdR * pom
+ + dGLJdR * pom+sgrad
gvdwc(k,i) = gvdwc(k,i) &
- dGCLdR * erhead(k) &
- dPOLdR1 * erhead_tail(k,1) &
- - dGLJdR * erhead(k)
+ - dGLJdR * erhead(k)-sgrad
gvdwc(k,j) = gvdwc(k,j) &
+ dGCLdR * erhead(k) &
+ dPOLdR1 * erhead_tail(k,1) &
- + dGLJdR * erhead(k)
+ + dGLJdR * erhead(k)+sgrad
END DO
RETURN
use comm_momo
use calc_data
- double precision facd3, adler,ecl,elj,epol
+ double precision facd3, adler,ecl,elj,epol,sgrad
alphapol2 = alphapol(itypj,itypi)
w1 = wqdip(1,itypi,itypj)
w2 = wqdip(2,itypi,itypj)
!c! derivative of ecl is Gcl
!c! dF/dr part
dGCLdR =sss_ele_cut*(- 2.0d0 * sparrow / Rhead**3.0d0 &
- + 4.0d0 * hawk / Rhead**5.0d0)+Ecl*sss_ele_grad
+ + 4.0d0 * hawk / Rhead**5.0d0)
!c! dF/dom1
dGCLdOM1 = (w1 * Qj) / (Rhead**2.0d0)
!c! dF/dom2
* (2.0d0 - 0.5d0 * ee2) ) &
/ (2.0d0 * fgb2)
dPOLdR2 = dPOLdFGB2 * dFGBdR2*sss_ele_cut
- epol=epol*sss_ele_cut
!c! dPOLdR2 = 0.0d0
dPOLdOM1 = dPOLdFGB2 * dFGBdOM1
!c! dPOLdOM1 = 0.0d0
!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)))*sss_ele_cut+Elj*sss_ele_grad
- elj=elj*sss_ele_cut
+ + (( 6.0d0*pis**6.0d0) /(Rhead**7.0d0)))*sss_ele_cut
!c!-------------------------------------------------------------------
!c! Return the results
!c! (see comments in Eqq)
DO k = 1, 3
condor = (erhead_tail(k,2) &
+ facd2 * (erhead_tail(k,2) - eagle * dC_norm(k,j+nres)))
-
+ sgrad=(epol+elj+ecl)*sss_ele_grad*rreal(k)*rij
pom = erhead(k)+facd1*(erhead(k)-erdxi*dC_norm(k,i+nres))
gvdwx(k,i) = gvdwx(k,i) &
- dGCLdR * pom &
- dPOLdR2 * (erhead_tail(k,2) &
-facd3 * (erhead_tail(k,2) - adler * dC_norm(k,i+nres))) &
- - dGLJdR * pom
+ - dGLJdR * pom-sgrad
pom = erhead(k)+facd2*(erhead(k)-erdxj*dC_norm(k,j+nres))
gvdwx(k,j) = gvdwx(k,j) &
+ dGCLdR * pom &
+ dPOLdR2 * condor &
- + dGLJdR * pom
+ + dGLJdR * pom+sgrad
gvdwc(k,i) = gvdwc(k,i) &
- dGCLdR * erhead(k) &
- dPOLdR2 * erhead_tail(k,2) &
- - dGLJdR * erhead(k)
+ - dGLJdR * erhead(k)-sgrad
gvdwc(k,j) = gvdwc(k,j) &
+ dGCLdR * erhead(k) &
+ dPOLdR2 * erhead_tail(k,2) &
- + dGLJdR * erhead(k)
+ + dGLJdR * erhead(k)+sgrad
END DO
RETURN
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
+ dGCLdR = (c1 - c2)*sss_ele_cut!+ECL*sss_ele_grad
!c! dECL/dom1
c1 = (-3.0d0 * w1 * om2 ) / (Rhead**3.0d0)
c2 = (-6.0d0 * w2) / (Rhead**6.0d0) &
DO k = 1, 3
pom = erhead(k)+facd1*(erhead(k)-erdxi*dC_norm(k,i+nres))
- gvdwx(k,i) = gvdwx(k,i) - dGCLdR * pom
+ gvdwx(k,i) = gvdwx(k,i)- dGCLdR * pom-(ecl*sss_ele_grad*Rreal(k)*rij)
pom = erhead(k)+facd2*(erhead(k)-erdxj*dC_norm(k,j+nres))
- gvdwx(k,j) = gvdwx(k,j) + dGCLdR * pom
+ gvdwx(k,j) = gvdwx(k,j)+ dGCLdR * pom+(ecl*sss_ele_grad*Rreal(k)*rij)
- gvdwc(k,i) = gvdwc(k,i) - dGCLdR * erhead(k)
- gvdwc(k,j) = gvdwc(k,j) + dGCLdR * erhead(k)
+ gvdwc(k,i) = gvdwc(k,i)- dGCLdR * erhead(k)-(ecl*sss_ele_grad*Rreal(k)*rij)
+ gvdwc(k,j) = gvdwc(k,j)+ dGCLdR * erhead(k)+(ecl*sss_ele_grad*Rreal(k)*rij)
END DO
RETURN
END SUBROUTINE edd
yi=c(2,nres+i)
zi=c(3,nres+i)
call to_box(xi,yi,zi)
- dxi=dc_norm(1,nres+i)
- dyi=dc_norm(2,nres+i)
- dzi=dc_norm(3,nres+i)
+ dxi=dc_norm(1,i)
+ dyi=dc_norm(2,i)
+ dzi=dc_norm(3,i)
xmedi=c(1,i)+0.5d0*dxi
ymedi=c(2,i)+0.5d0*dyi
zmedi=c(3,i)+0.5d0*dzi
return
end subroutine make_cat_pep_list
+ subroutine make_lip_pep_list
+ include 'mpif.h'
+ real(kind=8) :: xi,yi,zi,xj,yj,zj,xj_safe,yj_safe,zj_safe,xj_temp,yj_temp,zj_temp
+ real(kind=8) :: xmedj,ymedj,zmedj,sslipi,ssgradlipi,faclipij2,sslipj,ssgradlipj
+ real(kind=8) :: dist_init, dist_temp,r_buff_list,dxi,dyi,dzi,xmedi,ymedi,zmedi
+ real(kind=8) :: dx_normi,dy_normi,dz_normi,dxj,dyj,dzj,dx_normj,dy_normj,dz_normj
+ real(kind=8) :: xja,yja,zja
+ integer:: contlistmartpi(300*nres),contlistmartpj(300*nres)
+ integer:: contlistmartsci(250*nres),contlistmartscj(250*nres)
+
+
+! integer :: newcontlistppi(200*nres),newcontlistppj(200*nres)
+ integer i,j,itypi,itypj,subchap,xshift,yshift,zshift,iint,ilist_martsc,&
+ ilist_martp,k,itmp
+ integer displ(0:nprocs),i_ilist_martsc(0:nprocs),ierr,&
+ i_ilist_martp(0:nprocs)
+! write(iout,*),"START make_pp",iatel_s,iatel_e,r_cut_ele+r_buff_list
+ ilist_martp=0
+ ilist_martsc=0
+
+
+ r_buff_list=6.0
+ itmp=0
+ do i=1,3
+ itmp=itmp+nres_molec(i)
+ enddo
+! go to 17
+! do i=1,nres_molec(1)-1 ! loop over all peptide groups needs parralelization
+ do i=ibond_start,ibond_end
+
+! print *,"I am in EVDW",i
+ itypi=iabs(itype(i,1))
+
+! if (i.ne.47) cycle
+ if ((itypi.eq.ntyp1).or.(itypi.eq.10)) cycle
+! itypi1=iabs(itype(i+1,1))
+ xi=c(1,nres+i)
+ yi=c(2,nres+i)
+ zi=c(3,nres+i)
+ call to_box(xi,yi,zi)
+ dxi=dc_norm(1,i)
+ dyi=dc_norm(2,i)
+ dzi=dc_norm(3,i)
+ xmedi=c(1,i)+0.5d0*dxi
+ ymedi=c(2,i)+0.5d0*dyi
+ zmedi=c(3,i)+0.5d0*dzi
+ call to_box(xmedi,ymedi,zmedi)
+
+! dsci_inv=vbld_inv(i+nres)
+ do j=itmp+1,itmp+nres_molec(4)
+ dxj=dc(1,j)
+ dyj=dc(2,j)
+ dzj=dc(3,j)
+ dx_normj=dc_norm(1,j)
+ dy_normj=dc_norm(2,j)
+ dz_normj=dc_norm(3,j)
+ xj=c(1,j)
+ yj=c(2,j)
+ zj=c(3,j)
+ call to_box(xj,yj,zj)
+! call lipid_layer(xj,yj,zj,sslipj,ssgradlipj)
+! faclipij2=(sslipi+sslipj)/2.0d0*lipscale**2+1.0d0
+ xja=boxshift(xj-xmedi,boxxsize)
+ yja=boxshift(yj-ymedi,boxysize)
+ zja=boxshift(zj-zmedi,boxzsize)
+ dist_init=xja**2+yja**2+zja**2
+ if (sqrt(dist_init).le.(r_cut_ele+r_buff_list)) then
+! Here the list is created
+ ilist_martp=ilist_martp+1
+! this can be substituted by cantor and anti-cantor
+ contlistmartpi(ilist_martp)=i
+ contlistmartpj(ilist_martp)=j
+ endif
+ xja=boxshift(xj-xi,boxxsize)
+ yja=boxshift(yj-yi,boxysize)
+ zja=boxshift(zj-zi,boxzsize)
+ dist_init=xja**2+yja**2+zja**2
+ if (sqrt(dist_init).le.(r_cut_ele+r_buff_list)) then
+! Here the list is created
+ ilist_martsc=ilist_martsc+1
+! this can be substituted by cantor and anti-cantor
+! write(iout,*) "have contact",i,j,ilist_martsc
+ contlistmartsci(ilist_martsc)=i
+ contlistmartscj(ilist_martsc)=j
+! write(iout,*) "have contact2",i,j,ilist_martsc,&
+! contlistmartsci(ilist_martsc),contlistmartscj(ilist_martsc)
+ endif
+! enddo
+ enddo
+ enddo
+#ifdef DEBUG
+ write (iout,*) "before MPIREDUCE",ilist_catsctran,ilist_catptran,&
+ ilist_catscnorm,ilist_catpnorm,ilist_catscang
+
+ do i=1,ilist_catsctran
+ 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
+ write (iout,*) i,contlistcatscnormi(i),contlistcatscnormj(i)
+ enddo
+ do i=1,ilist_catpnorm
+ write (iout,*) i,contlistcatpnormi(i),contlistcatscnormj(i)
+ enddo
+ do i=1,ilist_catscang
+ write (iout,*) i,contlistcatscangi(i),contlistcatscangi(i)
+ enddo
+
+
+#endif
+ if (nfgtasks.gt.1)then
+
+! write(iout,*) "before bcast",g_ilist_sc
+! call MPI_Bcast(g_ilist_sc,1,MPI_INT,king,FG_COMM)
+
+ call MPI_Reduce(ilist_martsc,g_ilist_martsc,1,&
+ MPI_INTEGER,MPI_SUM,king,FG_COMM,IERR)
+! write(iout,*) "before bcast",g_ilist_sc
+ call MPI_Gather(ilist_martsc,1,MPI_INTEGER,&
+ i_ilist_martsc,1,MPI_INTEGER,king,FG_COMM,IERR)
+ displ(0)=0
+ do i=1,nfgtasks-1,1
+ displ(i)=i_ilist_martsc(i-1)+displ(i-1)
+ enddo
+! write(iout,*) "before gather",displ(0),displ(1)
+ call MPI_Gatherv(contlistmartsci,ilist_martsc,MPI_INTEGER,&
+ newcontlistmartsci,i_ilist_martsc,displ,MPI_INTEGER,&
+ king,FG_COMM,IERR)
+ call MPI_Gatherv(contlistmartscj,ilist_martsc,MPI_INTEGER,&
+ newcontlistmartscj,i_ilist_martsc,displ,MPI_INTEGER,&
+ king,FG_COMM,IERR)
+ call MPI_Bcast(g_ilist_martsc,1,MPI_INT,king,FG_COMM,IERR)
+! write(iout,*) "before bcast",g_ilist_sc
+! call MPI_Bcast(g_ilist_sc,1,MPI_INT,king,FG_COMM)
+ call MPI_Bcast(newcontlistmartsci,g_ilist_martsc,MPI_INT,king,FG_COMM,IERR)
+ call MPI_Bcast(newcontlistmartscj,g_ilist_martsc,MPI_INT,king,FG_COMM,IERR)
+
+
+
+ call MPI_Reduce(ilist_martp,g_ilist_martp,1,&
+ MPI_INTEGER,MPI_SUM,king,FG_COMM,IERR)
+! write(iout,*) "before bcast",g_ilist_sc
+ call MPI_Gather(ilist_martp,1,MPI_INTEGER,&
+ i_ilist_martp,1,MPI_INTEGER,king,FG_COMM,IERR)
+ displ(0)=0
+ do i=1,nfgtasks-1,1
+ displ(i)=i_ilist_martp(i-1)+displ(i-1)
+ enddo
+! write(iout,*) "before gather",displ(0),displ(1)
+ call MPI_Gatherv(contlistmartpi,ilist_martp,MPI_INTEGER,&
+ newcontlistmartpi,i_ilist_martp,displ,MPI_INTEGER,&
+ king,FG_COMM,IERR)
+ call MPI_Gatherv(contlistmartpj,ilist_martp,MPI_INTEGER,&
+ newcontlistmartpj,i_ilist_martp,displ,MPI_INTEGER,&
+ king,FG_COMM,IERR)
+ call MPI_Bcast(g_ilist_martp,1,MPI_INT,king,FG_COMM,IERR)
+! write(iout,*) "before bcast",g_ilist_sc
+! call MPI_Bcast(g_ilist_sc,1,MPI_INT,king,FG_COMM)
+ call MPI_Bcast(newcontlistmartpi,g_ilist_martp,MPI_INT,king,FG_COMM,IERR)
+ call MPI_Bcast(newcontlistmartpj,g_ilist_martp,MPI_INT,king,FG_COMM,IERR)
+
+
+
+ else
+ g_ilist_martsc=ilist_martsc
+ g_ilist_martp=ilist_martp
+
+
+ do i=1,ilist_martsc
+ newcontlistmartsci(i)=contlistmartsci(i)
+ newcontlistmartscj(i)=contlistmartscj(i)
+ enddo
+ do i=1,ilist_martp
+ newcontlistmartpi(i)=contlistmartpi(i)
+ newcontlistmartpj(i)=contlistmartpj(i)
+ enddo
+ endif
+ call int_bounds(g_ilist_martsc,g_listmartsc_start,g_listmartsc_end)
+ call int_bounds(g_ilist_martp,g_listmartp_start,g_listmartp_end)
+! print *,"TUTU",g_listcatscang_start,g_listcatscang_end,i,j,g_ilist_catscangf,myrank
+
+#ifdef DEBUG
+ write (iout,*) "after MPIREDUCE",ilist_catsctran,ilist_catptran, &
+ ilist_catscnorm,ilist_catpnorm
+
+ do i=1,g_ilist_catsctran
+ write (iout,*) i,newcontlistcatsctrani(i),newcontlistcatsctranj(i)
+ enddo
+ do i=1,g_ilist_catptran
+ write (iout,*) i,newcontlistcatptrani(i),newcontlistcatsctranj(i)
+ enddo
+ do i=1,g_ilist_catscnorm
+ write (iout,*) i,newcontlistcatscnormi(i),newcontlistcatscnormj(i)
+ enddo
+ do i=1,g_ilist_catpnorm
+ write (iout,*) i,newcontlistcatpnormi(i),newcontlistcatscnormj(i)
+ enddo
+ do i=1,g_ilist_catscang
+ write (iout,*) i,newcontlistcatscangi(i),newcontlistcatscangj(i)
+#endif
+ return
+ end subroutine make_lip_pep_list
+
+
subroutine make_cat_cat_list
include 'mpif.h'
real(kind=8) :: xi,yi,zi,xj,yj,zj,xj_safe,yj_safe,zj_safe,xj_temp,yj_temp,zj_temp
#endif
-!--------------------------------------------------------------------------
+
+!-----------LIPID-MARTINI-UNRES-PROTEIN
+
+! new for K+
+ subroutine elip_prot(evdw)
+! subroutine emart_prot2(emartion_prot)
+ use calc_data
+ use comm_momo
+
+ logical :: lprn
+!el local variables
+ integer :: iint,itypi1,subchap,isel,itmp
+ real(kind=8) :: rrij,xi,yi,zi,sig,rij_shift,e1,e2,sigm,epsi
+ real(kind=8) :: evdw,aa,bb
+ 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,ki
+ real(kind=8) :: fracinbuf
+ real (kind=8) :: escpho
+ real (kind=8),dimension(4):: ener
+ real(kind=8) :: b1,b2,egb
+ real(kind=8) :: Fisocav,ECL,Elj,Equad,Epol,eheadtail,&
+ Lambf,&
+ Chif,ChiLambf,Fcav,dFdR,dFdOM1,&
+ emartions_prot_amber,dFdOM2,dFdL,dFdOM12,&
+ federmaus,&
+ d1i,d1j
+! real(kind=8),dimension(3,2)::erhead_tail
+! real(kind=8),dimension(3) :: Rhead_distance,ertail,erhead,Rtail_distance
+ real(kind=8) :: facd4, adler, Fgb, facd3
+ integer troll,jj,istate
+ real (kind=8) :: dcosom1(3),dcosom2(3)
+ real(kind=8) ::locbox(3)
+ locbox(1)=boxxsize
+ locbox(2)=boxysize
+ locbox(3)=boxzsize
+
+ evdw=0.0D0
+ if (nres_molec(4).eq.0) return
+ eps_out=80.0d0
+! sss_ele_cut=1.0d0
+
+ itmp=0
+ do i=1,4
+ itmp=itmp+nres_molec(i)
+ 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 ki=g_listmartsc_start,g_listmartsc_end
+ i=newcontlistmartsci(ki)
+ j=newcontlistmartscj(ki)
+
+! print *,"I am in EVDW",i
+ itypi=iabs(itype(i,1))
+
+! if (i.ne.47) cycle
+ if ((itypi.eq.ntyp1).or.(itypi.eq.10)) cycle
+ itypi1=iabs(itype(i+1,1))
+ xi=c(1,nres+i)
+ yi=c(2,nres+i)
+ zi=c(3,nres+i)
+ call to_box(xi,yi,zi)
+ call lipid_layer(xi,yi,zi,sslipi,ssgradlipi)
+ dxi=dc_norm(1,nres+i)
+ 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)
+
+! Calculate SC interaction energy.
+ itypj=iabs(itype(j,4))
+ if ((itypj.gt.ntyp_molec(4))) cycle
+ CALL elgrad_init_mart(eheadtail,Egb,Ecl,Elj,Equad,Epol)
+! print *,i,j,"after elgrad"
+ dscj_inv=0.0
+ xj=c(1,j)
+ yj=c(2,j)
+ zj=c(3,j)
+
+ call to_box(xj,yj,zj)
+! write(iout,*) "xi,yi,zi,xj,yj,zj", xi,yi,zi,xj,yj,zj
+
+! call lipid_layer(xj,yj,zj,sslipj,ssgradlipj)
+! aa=aa_lip(itypi,itypj)*(sslipi+sslipj)/2.0d0 &
+! +aa_aq(itypi,itypj)*(2.0d0-sslipi-sslipj)/2.0d0
+! bb=bb_lip(itypi,itypj)*(sslipi+sslipj)/2.0d0 &
+! +bb_aq(itypi,itypj)*(2.0d0-sslipi-sslipj)/2.0d0
+ xj=boxshift(xj-xi,boxxsize)
+ yj=boxshift(yj-yi,boxysize)
+ zj=boxshift(zj-zi,boxzsize)
+! write(iout,*) "xj,yj,zj", xj,yj,zj,boxxsize
+ rreal(1)=xj
+ rreal(2)=yj
+ rreal(3)=zj
+ 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 )
+
+ itypi = itype(i,1)
+ itypj = itype(j,4)
+! Parameters from fitting the analitical expressions to the PMF obtained by umbrella
+! sampling performed with amber package
+! alf1 = 0.0d0
+! alf2 = 0.0d0
+! alf12 = 0.0d0
+! a12sq = rborn(itypi,itypj) * rborn(itypj,itypi)
+ chi1 = chi1mart(itypi,itypj)
+ chis1 = chis1mart(itypi,itypj)
+ chip1 = chipp1mart(itypi,itypj)
+! chi1=0.0d0
+! chis1=0.0d0
+! chip1=0.0d0
+ chi2=0.0
+ chip2=0.0
+ chis2=0.0
+! chis2 = chis(itypj,itypi)
+ chis12 = chis1 * chis2
+ sig1 = sigmap1mart(itypi,itypj)
+ sig2=0.0d0
+! sig2 = sigmap2(itypi,itypj)
+! alpha factors from Fcav/Gcav
+ b1cav = alphasurmart(1,itypi,itypj)
+ b2cav = alphasurmart(2,itypi,itypj)
+ b3cav = alphasurmart(3,itypi,itypj)
+ b4cav = alphasurmart(4,itypi,itypj)
+
+! b1cav=0.0d0
+! b2cav=0.0d0
+! b3cav=0.0d0
+! b4cav=0.0d0
+
+! used to determine whether we want to do quadrupole calculations
+ eps_in = epsintabmart(itypi,itypj)
+ if (eps_in.eq.0.0) eps_in=1.0
+
+ eps_inout_fac = ( (1.0d0/eps_in) - (1.0d0/eps_out))
+! Rtail = 0.0d0
+
+ DO k = 1, 3
+ ctail(k,1)=c(k,i+nres)
+ ctail(k,2)=c(k,j)
+ END DO
+ call to_box(ctail(1,1),ctail(2,1),ctail(3,1))
+ call to_box(ctail(1,2),ctail(2,2),ctail(3,2))
+!c! tail distances will be themselves usefull elswhere
+!c1 (in Gcav, for example)
+ do k=1,3
+ Rtail_distance(k) = boxshift(ctail(k,2) - ctail(k,1),locbox(k))
+ enddo
+ Rtail = dsqrt( &
+ (Rtail_distance(1)*Rtail_distance(1)) &
+ + (Rtail_distance(2)*Rtail_distance(2)) &
+ + (Rtail_distance(3)*Rtail_distance(3)))
+! tail lomartion and distance calculations
+! dhead1
+ d1 = dheadmart(1, 1, itypi, itypj)
+! d2 = dhead(2, 1, itypi, itypj)
+ DO k = 1,3
+! lomartion of polar head is computed by taking hydrophobic centre
+! and moving by a d1 * dc_norm vector
+! see unres publimartions for very informative images
+ chead(k,1) = c(k, i+nres) + d1 * dc_norm(k, i+nres)
+ chead(k,2) = c(k, j)
+ enddo
+ call to_box(chead(1,1),chead(2,1),chead(3,1))
+ call to_box(chead(1,2),chead(2,2),chead(3,2))
+! write(iout,*) "TEST",chead(1,1),chead(2,1),chead(3,1),dc_norm(k, i+nres),d1
+! distance
+! Rsc_distance(k) = dabs(c(k, i+nres) - c(k, j+nres))
+! Rsc(k) = Rsc_distance(k) * Rsc_distance(k)
+ do k=1,3
+ Rhead_distance(k) = boxshift(chead(k,2) - chead(k,1),locbox(k))
+ END DO
+! pitagoras (root of sum of squares)
+ Rhead = dsqrt( &
+ (Rhead_distance(1)*Rhead_distance(1)) &
+ + (Rhead_distance(2)*Rhead_distance(2)) &
+ + (Rhead_distance(3)*Rhead_distance(3)))
+!-------------------------------------------------------------------
+! zero everything that should be zero'ed
+ evdwij = 0.0d0
+ ECL = 0.0d0
+ Elj = 0.0d0
+ Equad = 0.0d0
+ Epol = 0.0d0
+ Fcav=0.0d0
+ eheadtail = 0.0d0
+ dGCLdOM1 = 0.0d0
+ dGCLdOM2 = 0.0d0
+ dGCLdOM12 = 0.0d0
+ dPOLdOM1 = 0.0d0
+ dPOLdOM2 = 0.0d0
+ Fcav = 0.0d0
+ Fisocav=0.0d0
+ dFdR = 0.0d0
+ dCAVdOM1 = 0.0d0
+ dCAVdOM2 = 0.0d0
+ dCAVdOM12 = 0.0d0
+ dscj_inv = 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)
+ 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
+ sqom1 = om1 * om1
+ sqom2 = om2 * om2
+ sqom12 = om12 * om12
+
+! now we calculate EGB - Gey-Berne
+! It will be summed up in evdwij and saved in evdw
+ sigsq = 1.0D0 / sigsq
+ sig = sig0ij * dsqrt(sigsq)
+! rij_shift = 1.0D0 / rij - sig + sig0ij
+ rij_shift = Rtail - sig + sig0ij
+ IF (rij_shift.le.0.0D0) THEN
+ evdw = 1.0D20
+ if (evdw.gt.1.0d6) then
+ write (*,'(2(1x,a3,i3),7f7.2)') &
+ restyp(itype(i,1),1),i,restyp(itype(j,1),1),j,&
+ 1.0d0/rij,Rtail,Rhead,rij_shift, sig, sig0ij,sigsq
+ write(*,*) facsig,faceps1_inv,om1,chiom1,chi1
+ write(*,*) "ANISO?!",chi1
+!evdwij,Fcav,Ecl,Egb,Epol,Fisocav,Elj,&
+! Equad,evdwij+Fcav+eheadtail,evdw
+ endif
+
+ RETURN
+ END IF
+ sigder = -sig * sigsq
+ rij_shift = 1.0D0 / rij_shift
+ fac = rij_shift**expon
+ c1 = fac * fac * aa_aq_mart(itypi,itypj)
+! print *,"ADAM",aa_aq(itypi,itypj)
+
+! c1 = 0.0d0
+ c2 = fac * bb_aq_mart(itypi,itypj)
+! c2 = 0.0d0
+ evdwij = eps1 * eps2rt * eps3rt * ( c1 + c2 )
+ eps2der = eps3rt * evdwij
+ eps3der = eps2rt * evdwij
+! evdwij = 4.0d0 * eps2rt * eps3rt * evdwij
+ evdwij = eps2rt * eps3rt * evdwij
+!#ifdef TSCSC
+! IF (bb_aq(itypi,itypj).gt.0) THEN
+! evdw_p = evdw_p + evdwij
+! ELSE
+! evdw_m = evdw_m + evdwij
+! END IF
+!#else
+ evdw = evdw &
+ + evdwij*sss_ele_cut
+!#endif
+ c1 = c1 * eps1 * eps2rt**2 * eps3rt**2
+ fac = -expon * (c1 + evdwij) * rij_shift
+ sigder = fac * sigder
+! Calculate distance derivative
+ 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
+ pom = 1.0d0 - chis1 * chis2 * sqom12
+ Lambf = (1.0d0 - (fac / pom))
+ Lambf = dsqrt(Lambf)
+ sparrow = 1.0d0 / dsqrt(sig1**2.0d0 + sig2**2.0d0)
+ Chif = Rtail * sparrow
+ ChiLambf = Chif * Lambf
+ eagle = dsqrt(ChiLambf)
+ bat = ChiLambf ** 11.0d0
+ top = b1cav * ( eagle + b2cav * ChiLambf - b3cav )
+ bot = 1.0d0 + b4cav * (ChiLambf ** 12.0d0)
+ botsq = bot * bot
+ Fcav = top / bot
+
+ dtop = b1cav * ((Lambf / (2.0d0 * eagle)) + (b2cav * Lambf))
+ dbot = 12.0d0 * b4cav * bat * Lambf
+ dFdR = ((dtop * bot - top * dbot) / botsq) * sparrow
+ 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 )
+ dCAVdOM2 = dFdL * ( dFdOM2 )
+ dCAVdOM12 = dFdL * ( dFdOM12 )
+
+ DO k= 1, 3
+ ertail(k) = Rtail_distance(k)/Rtail
+ END DO
+ erdxi = scalar( ertail(1), dC_norm(1,i+nres) )
+ erdxj = scalar( ertail(1), dC_norm(1,j) )
+ facd1 = dtailmart(1,itypi,itypj) * vbld_inv(i+nres)
+ facd2 = dtailmart(2,itypi,itypj) * vbld_inv(j)
+ DO k = 1, 3
+ pom = ertail(k)-facd1*(ertail(k)-erdxi*dC_norm(k,i+nres))
+ gradpepmartx(k,i) = gradpepmartx(k,i) &
+ - (( dFdR + gg(k) ) * pom)*sss_ele_cut&
+ -(evdwij+Fcav)*rij*sss_ele_grad*rreal(k)
+
+ pom = ertail(k)-facd2*(ertail(k)-erdxj*dC_norm(k,j))
+! gvdwx(k,j) = gvdwx(k,j) &
+! + (( dFdR + gg(k) ) * pom)
+ gradpepmart(k,i) = gradpepmart(k,i) &
+ - (( dFdR + gg(k) ) * ertail(k))*sss_ele_cut&
+ -(evdwij+Fcav)*rij*sss_ele_grad*rreal(k)
+
+ gradpepmart(k,j) = gradpepmart(k,j) &
+ + (( dFdR + gg(k) ) * ertail(k))*sss_ele_cut&
+ +(evdwij+Fcav)*rij*sss_ele_grad*rreal(k)
+
+ gg(k) = 0.0d0
+ ENDDO
+!c! Compute head-head and head-tail energies for each state
+!! if (.false.) then ! turn off electrostatic
+ isel = iabs(Qi)+iabs(Qj)
+ if ((itype(j,4).gt.4).and.(itype(j,4).lt.14)) isel=isel+2
+! isel=0
+! if (isel.eq.2) isel=0
+ IF (isel.le.1) THEN
+ eheadtail = 0.0d0
+ ELSE IF (isel.eq.3) THEN
+ if (iabs(Qj).eq.1) then
+ CALL edq_mart(ecl, elj, epol)
+ eheadtail = ECL + elj + epol
+ else
+ 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_mart(ecl,elj,epol)
+ eheadtail = ECL + elj + epol
+ endif
+ ELSE IF ((isel.eq.2)) THEN
+ if (iabs(Qi).ne.1) then
+ eheadtail=0.0d0
+ else
+ 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_mart(Ecl,Egb,Epol,Fisocav,Elj)
+ eheadtail = ECL + Egb + Epol + Fisocav + Elj
+ endif
+ ELSE IF (isel.eq.4) then
+ call edd_mart(ecl)
+ eheadtail = ECL
+ ENDIF
+! write(iout,*) "not yet implemented",j,itype(j,5)
+!! endif ! turn off electrostatic
+ evdw = evdw + (Fcav + eheadtail)*sss_ele_cut
+! if (evdw.gt.1.0d6) then
+! write (*,'(2(1x,a3,i3),3f6.2,10f16.7)') &
+! restyp(itype(i,1),1),i,restyp(itype(j,1),1),j,&
+! 1.0d0/rij,Rtail,Rhead,evdwij,Fcav,Ecl,Egb,Epol,Fisocav,Elj,&
+! Equad,evdwij+Fcav+eheadtail,evdw
+! endif
+
+ IF (energy_dec) write (iout,'(2(1x,a3,i3),3f6.2,10f16.7)') &
+ restyp(itype(i,1),1),i,restyp(itype(j,1),1),j,&
+ 1.0d0/rij,Rtail,Rhead,evdwij,Fcav,Ecl,Egb,Epol,Fisocav,Elj,&
+ Equad,evdwij+Fcav+eheadtail,evdw
+! evdw = evdw + Fcav + eheadtail
+ if (energy_dec) write(iout,*) "FCAV", &
+ sig1,sig2,b1cav,b2cav,b3cav,b4cav
+! print *,"before sc_grad_mart", i,j, gradpepmart(1,j)
+! iF (nstate(itypi,itypj).eq.1) THEN
+ CALL sc_grad_mart
+! print *,"after sc_grad_mart", i,j, gradpepmart(1,j)
+
+! END IF
+!c!-------------------------------------------------------------------
+!c! NAPISY KONCOWE
+ END DO ! j
+! 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
+! do i=ibond_start,ibond_end
+
+ do ki=g_listmartp_start,g_listmartp_end
+ i=newcontlistmartpi(ki)
+ j=newcontlistmartpj(ki)
+
+! print *,"I am in EVDW",i
+ itypi=10 ! the peptide group parameters are for glicine
+
+! if (i.ne.47) cycle
+ if ((itype(i,1).eq.ntyp1).or.itype(i+1,1).eq.ntyp1) cycle
+ itypi1=iabs(itype(i+1,1))
+ xi=(c(1,i)+c(1,i+1))/2.0
+ yi=(c(2,i)+c(2,i+1))/2.0
+ zi=(c(3,i)+c(3,i+1))/2.0
+ call to_box(xi,yi,zi)
+ dxi=dc_norm(1,i)
+ 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)
+
+! Calculate SC interaction energy.
+ itypj=iabs(itype(j,4))
+ if ((itypj.gt.ntyp_molec(4))) cycle
+ CALL elgrad_init_mart_pep(eheadtail,Egb,Ecl,Elj,Equad,Epol)
+
+ dscj_inv=0.0
+ xj=c(1,j)
+ yj=c(2,j)
+ zj=c(3,j)
+ call to_box(xj,yj,zj)
+ xj=boxshift(xj-xi,boxxsize)
+ yj=boxshift(yj-yi,boxysize)
+ zj=boxshift(zj-zi,boxzsize)
+ rreal(1)=xj
+ rreal(2)=yj
+ rreal(3)=zj
+
+ dist_init=(xj-xi)**2+(yj-yi)**2+(zj-zi)**2
+
+ dxj = 0.0d0! dc_norm( 1, nres+j )
+ dyj = 0.0d0!dc_norm( 2, nres+j )
+ dzj = 0.0d0! dc_norm( 3, nres+j )
+
+ itypi = 10
+ itypj = itype(j,4)
+! Parameters from fitting the analitical expressions to the PMF obtained by umbrella
+! sampling performed with amber package
+! alf1 = 0.0d0
+! alf2 = 0.0d0
+! alf12 = 0.0d0
+! a12sq = rborn(itypi,itypj) * rborn(itypj,itypi)
+ chi1 = chi1mart(itypi,itypj)
+ chis1 = chis1mart(itypi,itypj)
+ chip1 = chipp1mart(itypi,itypj)
+! chi1=0.0d0
+! chis1=0.0d0
+! chip1=0.0d0
+ chi2=0.0
+ chip2=0.0
+ chis2=0.0
+! chis2 = chis(itypj,itypi)
+ chis12 = chis1 * chis2
+ sig1 = sigmap1mart(itypi,itypj)
+ sig2=0.0
+! sig2 = sigmap2(itypi,itypj)
+! alpha factors from Fcav/Gcav
+ b1cav = alphasurmart(1,itypi,itypj)
+ b2cav = alphasurmart(2,itypi,itypj)
+ b3cav = alphasurmart(3,itypi,itypj)
+ b4cav = alphasurmart(4,itypi,itypj)
+
+! used to determine whether we want to do quadrupole calculations
+ eps_in = epsintabmart(itypi,itypj)
+ if (eps_in.eq.0.0) eps_in=1.0
+
+ eps_inout_fac = ( (1.0d0/eps_in) - (1.0d0/eps_out))
+! Rtail = 0.0d0
+
+ DO k = 1, 3
+ ctail(k,1)=(c(k,i)+c(k,i+1))/2.0
+ ctail(k,2)=c(k,j)
+ END DO
+ call to_box(ctail(1,1),ctail(2,1),ctail(3,1))
+ call to_box(ctail(1,2),ctail(2,2),ctail(3,2))
+!c! tail distances will be themselves usefull elswhere
+!c1 (in Gcav, for example)
+ do k=1,3
+ Rtail_distance(k) = boxshift(ctail(k,2) - ctail(k,1),locbox(k))
+ enddo
+
+!c! tail distances will be themselves usefull elswhere
+!c1 (in Gcav, for example)
+ Rtail = dsqrt( &
+ (Rtail_distance(1)*Rtail_distance(1)) &
+ + (Rtail_distance(2)*Rtail_distance(2)) &
+ + (Rtail_distance(3)*Rtail_distance(3)))
+! tail lomartion and distance calculations
+! dhead1
+ d1 = dheadmart(1, 1, itypi, itypj)
+! print *,"d1",d1
+! d1=0.0d0
+! d2 = dhead(2, 1, itypi, itypj)
+ DO k = 1,3
+! lomartion of polar head is computed by taking hydrophobic centre
+! and moving by a d1 * dc_norm vector
+! see unres publimartions for very informative images
+ chead(k,1) = (c(k, i)+c(k,i+1))/2.0 + d1 * dc_norm(k, i)
+ chead(k,2) = c(k, j)
+ ENDDO
+! distance
+! Rsc_distance(k) = dabs(c(k, i+nres) - c(k, j+nres))
+! Rsc(k) = Rsc_distance(k) * Rsc_distance(k)
+ call to_box(chead(1,1),chead(2,1),chead(3,1))
+ call to_box(chead(1,2),chead(2,2),chead(3,2))
+
+! distance
+! Rsc_distance(k) = dabs(c(k, i+nres) - c(k, j+nres))
+! Rsc(k) = Rsc_distance(k) * Rsc_distance(k)
+ do k=1,3
+ Rhead_distance(k) = boxshift(chead(k,2) - chead(k,1),locbox(k))
+ END DO
+
+! pitagoras (root of sum of squares)
+ Rhead = dsqrt( &
+ (Rhead_distance(1)*Rhead_distance(1)) &
+ + (Rhead_distance(2)*Rhead_distance(2)) &
+ + (Rhead_distance(3)*Rhead_distance(3)))
+!-------------------------------------------------------------------
+! zero everything that should be zero'ed
+ evdwij = 0.0d0
+ ECL = 0.0d0
+ Elj = 0.0d0
+ Equad = 0.0d0
+ Epol = 0.0d0
+ Fcav=0.0d0
+ eheadtail = 0.0d0
+ dGCLdOM1 = 0.0d0
+ dGCLdOM2 = 0.0d0
+ dGCLdOM12 = 0.0d0
+ dPOLdOM1 = 0.0d0
+ dPOLdOM2 = 0.0d0
+ Fcav = 0.0d0
+ dFdR = 0.0d0
+ dCAVdOM1 = 0.0d0
+ dCAVdOM2 = 0.0d0
+ dCAVdOM12 = 0.0d0
+ 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)
+ 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
+ om2=0.0d0
+ om12=0.0d0
+ sqom1 = om1 * om1
+ sqom2 = om2 * om2
+ sqom12 = om12 * om12
+
+! now we calculate EGB - Gey-Berne
+! It will be summed up in evdwij and saved in evdw
+ sigsq = 1.0D0 / sigsq
+ sig = sig0ij * dsqrt(sigsq)
+! rij_shift = 1.0D0 / rij - sig + sig0ij
+ rij_shift = Rtail - sig + sig0ij
+ IF (rij_shift.le.0.0D0) THEN
+ evdw = 1.0D20
+! if (evdw.gt.1.0d6) then
+! write (*,'(2(1x,a3,i3),6f6.2)') &
+! restyp(itype(i,1),1),i,restyp(itype(j,1),1),j,&
+! 1.0d0/rij,Rtail,Rhead,rij_shift, sig, sig0ij
+!evdwij,Fcav,Ecl,Egb,Epol,Fisocav,Elj,&
+! Equad,evdwij+Fcav+eheadtail,evdw
+! endif
+ RETURN
+ END IF
+ sigder = -sig * sigsq
+ rij_shift = 1.0D0 / rij_shift
+ fac = rij_shift**expon
+ c1 = fac * fac * aa_aq_mart(itypi,itypj)
+! print *,"ADAM",aa_aq(itypi,itypj)
+
+! c1 = 0.0d0
+ c2 = fac * bb_aq_mart(itypi,itypj)
+! c2 = 0.0d0
+ evdwij = eps1 * eps2rt * eps3rt * ( c1 + c2 )
+ eps2der = eps3rt * evdwij
+ eps3der = eps2rt * evdwij
+! evdwij = 4.0d0 * eps2rt * eps3rt * evdwij
+ evdwij = eps2rt * eps3rt * evdwij
+!#ifdef TSCSC
+! IF (bb_aq(itypi,itypj).gt.0) THEN
+! evdw_p = evdw_p + evdwij
+! ELSE
+! evdw_m = evdw_m + evdwij
+! END IF
+!#else
+ evdw = evdw &
+ + evdwij*sss_ele_cut
+!#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
+
+ fac = chis1 * sqom1 + chis2 * sqom2 &
+ - 2.0d0 * chis12 * om1 * om2 * om12
+
+ pom = 1.0d0 - chis1 * chis2 * sqom12
+! print *,"TUT2",fac,chis1,sqom1,pom
+ Lambf = (1.0d0 - (fac / pom))
+ Lambf = dsqrt(Lambf)
+ sparrow = 1.0d0 / dsqrt(sig1**2.0d0 + sig2**2.0d0)
+ Chif = Rtail * sparrow
+ ChiLambf = Chif * Lambf
+ eagle = dsqrt(ChiLambf)
+ bat = ChiLambf ** 11.0d0
+ top = b1cav * ( eagle + b2cav * ChiLambf - b3cav )
+ bot = 1.0d0 + b4cav * (ChiLambf ** 12.0d0)
+ botsq = bot * bot
+ Fcav = top / bot
+
+ dtop = b1cav * ((Lambf / (2.0d0 * eagle)) + (b2cav * Lambf))
+ dbot = 12.0d0 * b4cav * bat * Lambf
+ dFdR = ((dtop * bot - top * dbot) / botsq) * sparrow
+ 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 )
+! dCAVdOM2 = dFdL * ( dFdOM2 )
+! dCAVdOM12 = dFdL * ( dFdOM12 )
+ dCAVdOM2=0.0d0
+ dCAVdOM12=0.0d0
+
+ DO k= 1, 3
+ ertail(k) = Rtail_distance(k)/Rtail
+ END DO
+ erdxi = scalar( ertail(1), dC_norm(1,i) )
+ erdxj = scalar( ertail(1), dC_norm(1,j) )
+ facd1 = dtailmart(1,itypi,itypj) * vbld_inv(i)
+ facd2 = dtailmart(2,itypi,itypj) * vbld_inv(j+nres)
+ DO k = 1, 3
+ pom = ertail(k)-facd1*(ertail(k)-erdxi*dC_norm(k,i))
+! gradpepmartx(k,i) = gradpepmartx(k,i) &
+! - (( dFdR + gg(k) ) * pom)
+ pom = ertail(k)-facd2*(ertail(k)-erdxj*dC_norm(k,j+nres))
+! gvdwx(k,j) = gvdwx(k,j) &
+! + (( dFdR + gg(k) ) * pom)
+ gradpepmart(k,i) = gradpepmart(k,i) &
+ - (( dFdR + gg(k) ) * ertail(k))/2.0d0*sss_ele_cut&
+ -(evdwij+Fcav)*rij*sss_ele_grad*rreal(k)*0.5d0
+ gradpepmart(k,i+1) = gradpepmart(k,i+1) &
+ - (( dFdR + gg(k) ) * ertail(k))/2.0d0*sss_ele_cut&
+ -(evdwij+Fcav)*rij*sss_ele_grad*rreal(k)*0.5d0
+
+ gradpepmart(k,j) = gradpepmart(k,j) &
+ + (( dFdR + gg(k) ) * ertail(k))*sss_ele_cut&
+ +(evdwij+Fcav)*rij*sss_ele_grad*rreal(k)
+
+ gg(k) = 0.0d0
+ ENDDO
+!c! Compute head-head and head-tail energies for each state
+!c! Dipole-charge interactions
+ isel = 2+iabs(Qj)
+ if ((itype(j,4).gt.4).and.(itype(j,4).lt.14)) isel=isel+2
+! if (isel.eq.4) isel=0
+ if (isel.le.2) then
+ eheadtail=0.0d0
+ ELSE if (isel.eq.3) then
+ CALL edq_mart_pep(ecl, elj, epol)
+ eheadtail = ECL + elj + epol
+! print *,"i,",i,eheadtail
+! eheadtail = 0.0d0
+ else
+!HERE WATER and other types of molecules solvents will be added
+! write(iout,*) "not yet implemented"
+ CALL edd_mart_pep(ecl)
+ eheadtail=ecl
+! CALL edd_mart_pep
+! eheadtail=0.0d0
+ endif
+ evdw = evdw +( Fcav + eheadtail)*sss_ele_cut
+! if (evdw.gt.1.0d6) then
+! write (*,'(2(1x,a3,i3),3f6.2,10f16.7)') &
+! restyp(itype(i,1),1),i,restyp(itype(j,1),1),j,&
+! 1.0d0/rij,Rtail,Rhead,evdwij,Fcav,Ecl,Egb,Epol,Fisocav,Elj,&
+! Equad,evdwij+Fcav+eheadtail,evdw
+! endif
+ IF (energy_dec) write (iout,'(2(1x,a3,i3),3f6.2,10f16.7)') &
+ restyp(itype(i,1),1),i,restyp(itype(j,1),1),j,&
+ 1.0d0/rij,Rtail,Rhead,evdwij,Fcav,Ecl,Egb,Epol,Fisocav,Elj,&
+ Equad,evdwij+Fcav+eheadtail,evdw
+! evdw = evdw + Fcav + eheadtail
+
+! iF (nstate(itypi,itypj).eq.1) THEN
+ CALL sc_grad_mart_pep
+! END IF
+!c!-------------------------------------------------------------------
+!c! NAPISY KONCOWE
+ END DO ! j
+! END DO ! i
+!c write (iout,*) "Number of loop steps in EGB:",ind
+!c energy_dec=.false.
+! print *,"EVDW KURW",evdw,nres
+ 23 continue
+! print *,"before leave sc_grad_mart", i,j, gradpepmart(1,nres-1)
+
+ return
+ end subroutine elip_prot
+
+ SUBROUTINE eqq_mart(Ecl,Egb,Epol,Fisocav,Elj)
+ use calc_data
+ use comm_momo
+ real (kind=8) :: facd3, facd4, federmaus, adler,&
+ Ecl,Egb,Epol,Fisocav,Elj,Fgb,debkap
+! integer :: k
+!c! Epol and Gpol analytical parameters
+ alphapol1 = alphapolmart(itypi,itypj)
+ alphapol2 = alphapolmart2(itypj,itypi)
+!c! Fisocav and Gisocav analytical parameters
+ al1 = alphisomart(1,itypi,itypj)
+ al2 = alphisomart(2,itypi,itypj)
+ al3 = alphisomart(3,itypi,itypj)
+ al4 = alphisomart(4,itypi,itypj)
+ csig = (1.0d0 &
+ / dsqrt(sigiso1mart(itypi, itypj)**2.0d0 &
+ + sigiso2mart(itypi,itypj)**2.0d0))
+!c!
+ pis = sig0headmart(itypi,itypj)
+ eps_head = epsheadmart(itypi,itypj)
+ Rhead_sq = Rhead * Rhead
+!c! R1 - distance between head of ith side chain and tail of jth sidechain
+!c! R2 - distance between head of jth side chain and tail of ith sidechain
+ R1 = 0.0d0
+ R2 = 0.0d0
+ DO k = 1, 3
+!c! Calculate head-to-tail distances needed by Epol
+ R1=R1+(ctail(k,2)-chead(k,1))**2
+ R2=R2+(chead(k,2)-ctail(k,1))**2
+ END DO
+!c! Pitagoras
+ R1 = dsqrt(R1)
+ R2 = dsqrt(R2)
+
+!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! Coulomb electrostatic interaction
+ Ecl = (332.0d0 * Qij) / Rhead
+!c! derivative of Ecl is Gcl...
+ dGCLdR = (-332.0d0 * Qij ) / Rhead_sq
+ dGCLdOM1 = 0.0d0
+ dGCLdOM2 = 0.0d0
+ dGCLdOM12 = 0.0d0
+
+ ee0 = dexp(-( Rhead_sq ) / (4.0d0 * a12sq))
+ Fgb = sqrt( ( Rhead_sq ) + a12sq * ee0)
+ debkap=debaykapmart(itypi,itypj)
+ if (energy_dec) write(iout,*) "egb",Qij,debkap,Fgb,a12sq,ee0
+ Egb = -(332.0d0 * Qij *&
+ (1.0/eps_in-dexp(-debkap*Fgb)/eps_out)) / Fgb
+! print *,"EGB WTF",Qij,eps_inout_fac,Fgb,itypi,itypj,eps_in,eps_out
+!c! Derivative of Egb is Ggb...
+ dGGBdFGB = -(-332.0d0 * Qij * &
+ (1.0/eps_in-dexp(-debkap*Fgb)/eps_out))/(Fgb*Fgb)&
+ -(332.0d0 * Qij *&
+ (dexp(-debkap*Fgb)*debkap/eps_out))/ Fgb
+ dFGBdR = ( Rhead * ( 2.0d0 - (0.5d0 * ee0) ) )/ ( 2.0d0 * Fgb )
+ dGGBdR = dGGBdFGB * dFGBdR
+!c!-------------------------------------------------------------------
+!c! Fisocav - isotropic cavity creation term
+!c! or "how much energy it costs to put charged head in water"
+ pom = Rhead * csig
+ top = al1 * (dsqrt(pom) + al2 * pom - al3)
+ bot = (1.0d0 + al4 * pom**12.0d0)
+ botsq = bot * bot
+ FisoCav = top / bot
+! write (*,*) "Rhead = ",Rhead
+! write (*,*) "csig = ",csig
+! write (*,*) "pom = ",pom
+! write (*,*) "al1 = ",al1
+! write (*,*) "al2 = ",al2
+! write (*,*) "al3 = ",al3
+! write (*,*) "al4 = ",al4
+! write (*,*) "top = ",top
+! write (*,*) "bot = ",bot
+!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
+!c!-------------------------------------------------------------------
+!c! Epol
+!c! Polarization energy - charged heads polarize hydrophobic "neck"
+ MomoFac1 = (1.0d0 - chi1 * sqom2)
+ MomoFac2 = (1.0d0 - chi2 * sqom1)
+ RR1 = ( R1 * R1 ) / MomoFac1
+ RR2 = ( R2 * R2 ) / MomoFac2
+ ee1 = exp(-( RR1 / (4.0d0 * a12sq) ))
+ ee2 = exp(-( RR2 / (4.0d0 * a12sq) ))
+ fgb1 = sqrt( RR1 + a12sq * ee1 )
+ fgb2 = sqrt( RR2 + a12sq * ee2 )
+ epol = 332.0d0 * eps_inout_fac * ( &
+ (( alphapol1 / fgb1 )**4.0d0)+((alphapol2/fgb2) ** 4.0d0 ))
+!c! epol = 0.0d0
+ dPOLdFGB1 = -(1328.0d0 * eps_inout_fac * alphapol1 ** 4.0d0)&
+ / (fgb1 ** 5.0d0)
+ dPOLdFGB2 = -(1328.0d0 * eps_inout_fac * alphapol2 ** 4.0d0)&
+ / (fgb2 ** 5.0d0)
+ dFGBdR1 = ( (R1 / MomoFac1)* ( 2.0d0 - (0.5d0 * ee1) ) )&
+ / ( 2.0d0 * fgb1 )
+ dFGBdR2 = ( (R2 / MomoFac2)* ( 2.0d0 - (0.5d0 * ee2) ) )&
+ / ( 2.0d0 * fgb2 )
+ dFGBdOM2 = (((R1 * R1 * chi1 * om2) / (MomoFac1 * MomoFac1))&
+ * ( 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!*sss_ele_cut+epol*sss_ele_grad
+!c! dPOLdR1 = 0.0d0
+ dPOLdR2 = dPOLdFGB2 * dFGBdR2!*sss_ele_cut+epol*sss_ele_grad
+!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! Lennard-Jones 6-12 interaction between heads
+ 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*(((-12.0d0*pis**12.0d0)/(Rhead**13.0d0))&
+ + (( 6.0d0*pis**6.0d0) /(Rhead**7.0d0)))
+!c!-------------------------------------------------------------------
+!c! Return the results
+!c! These things do the dRdX derivatives, that is
+!c! allow us to change what we see from function that changes with
+!c! distance to function that changes with LOCATION (of the interaction
+!c! site)
+ DO k = 1, 3
+ erhead(k) = Rhead_distance(k)/Rhead
+ erhead_tail(k,1) = ((ctail(k,2)-chead(k,1))/R1)
+ erhead_tail(k,2) = ((chead(k,2)-ctail(k,1))/R2)
+ END DO
+
+ erdxi = scalar( erhead(1), dC_norm(1,i+nres) )
+ erdxj = scalar( erhead(1), dC_norm(1,j) )
+ bat = scalar( erhead_tail(1,1), dC_norm(1,i+nres) )
+ federmaus = scalar(erhead_tail(1,1),dC_norm(1,j))
+ eagle = scalar( erhead_tail(1,2), dC_norm(1,j) )
+ adler = scalar( erhead_tail(1,2), dC_norm(1,i+nres) )
+ facd1 = d1 * vbld_inv(i+nres)
+ facd2 = d2 * vbld_inv(j)
+ facd3 = dtailmart(1,itypi,itypj) * vbld_inv(i+nres)
+ facd4 = dtailmart(2,itypi,itypj) * vbld_inv(j)
+
+!c! Now we add appropriate partial derivatives (one in each dimension)
+ DO k = 1, 3
+ hawk = (erhead_tail(k,1) + &
+ facd1 * (erhead_tail(k,1) - bat * dC_norm(k,i+nres)))
+ condor = (erhead_tail(k,2) + &
+ facd2 * (erhead_tail(k,2) - eagle * dC_norm(k,j)))
+
+ pom = erhead(k)+facd1*(erhead(k)-erdxi*dC_norm(k,i+nres))
+ gradpepmartx(k,i) = gradpepmartx(k,i) &
+ +sss_ele_cut*(- dGCLdR * pom&
+ - dGGBdR * pom&
+ - dGCVdR * pom&
+ - dPOLdR1 * hawk&
+ - dPOLdR2 * (erhead_tail(k,2)&
+ -facd3 * (erhead_tail(k,2) - adler * dC_norm(k,i+nres)))&
+ - dGLJdR * pom)-&
+ sss_ele_grad*rij*rreal(k)*(Ecl+Egb+Epol+Fisocav+Elj)
+
+ pom = erhead(k)+facd2*(erhead(k)-erdxj*dC_norm(k,j))
+! gradpepmartx(k,j) = gradpepmartx(k,j)+ dGCLdR * pom&
+! + dGGBdR * pom+ dGCVdR * pom&
+! + dPOLdR1 * (erhead_tail(k,1)&
+! -facd4 * (erhead_tail(k,1) - federmaus * dC_norm(k,j)))&
+! + dPOLdR2 * condor + dGLJdR * pom
+
+ gradpepmart(k,i) = gradpepmart(k,i) + &
+ sss_ele_cut*(- dGCLdR * erhead(k)&
+ - dGGBdR * erhead(k)&
+ - dGCVdR * erhead(k)&
+ - dPOLdR1 * erhead_tail(k,1)&
+ - dPOLdR2 * erhead_tail(k,2)&
+ - dGLJdR * erhead(k))&
+ - sss_ele_grad*rij*rreal(k)*(Ecl+Egb+Epol+Fisocav+Elj)
+
+
+ gradpepmart(k,j) = gradpepmart(k,j) + &
+ sss_ele_cut*( dGCLdR * erhead(k) &
+ + dGGBdR * erhead(k) &
+ + dGCVdR * erhead(k) &
+ + dPOLdR1 * erhead_tail(k,1) &
+ + dPOLdR2 * erhead_tail(k,2)&
+ + dGLJdR * erhead(k))&
+ +sss_ele_grad*rij*rreal(k)*(Ecl+Egb+Epol+Fisocav+Elj)
+ END DO
+ RETURN
+ END SUBROUTINE eqq_mart
+
+ SUBROUTINE eqd_mart(Ecl,Elj,Epol)
+ use calc_data
+ use comm_momo
+ double precision facd4, federmaus,ecl,elj,epol
+ alphapol1 = alphapolmart(itypi,itypj)
+ w1 = wqdipmart(1,itypi,itypj)
+ w2 = wqdipmart(2,itypi,itypj)
+ pis = sig0headmart(itypi,itypj)
+ eps_head = epsheadmart(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)
+!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
+!c! dPOLdR1 = 0.0d0
+ dPOLdOM1 = 0.0d0
+! dPOLdOM2 = dPOLdFGB1 * dFGBdOM2
+ dPOLdOM2 = 0.0d0
+!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)))
+ 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))
+ gradpepmartx(k,i) = gradpepmartx(k,i) &
+ - dGCLdR * pom&
+ - dPOLdR1 * hawk &
+ - dGLJdR * pom&
+ -(Ecl+Elj+Epol)*sss_ele_grad*rreal(k)*rij
+
+
+! pom = erhead(k)+facd2*(erhead(k)-erdxj*dC_norm(k,j+nres))
+! gradpepmartx(k,j) = gradpepmartx(k,j) &
+! + dGCLdR * pom &
+! + dPOLdR1 * (erhead_tail(k,1) &
+! -facd4 * (erhead_tail(k,1) - federmaus * dC_norm(k,j+nres))) &
+! + dGLJdR * pom
+
+
+ gradpepmart(k,i) = gradpepmart(k,i) &
+ - dGCLdR * erhead(k) &
+ - dPOLdR1 * erhead_tail(k,1) &
+ - dGLJdR * erhead(k)&
+ -(Ecl+Elj+Epol)*sss_ele_grad*rreal(k)*rij
+
+
+ gradpepmart(k,j) = gradpepmart(k,j) &
+ + dGCLdR * erhead(k) &
+ + dPOLdR1 * erhead_tail(k,1) &
+ + dGLJdR * erhead(k)&
+ +(Ecl+Elj+Epol)*sss_ele_grad*rreal(k)*rij
+
+
+ END DO
+ RETURN
+ END SUBROUTINE eqd_mart
+
+ SUBROUTINE edq_mart(Ecl,Elj,Epol)
+ use comm_momo
+ use calc_data
+
+ double precision facd3, adler,ecl,elj,epol
+ alphapol2 = alphapolmart(itypi,itypj)
+ w1 = wqdipmart(1,itypi,itypj)
+ w2 = wqdipmart(2,itypi,itypj)
+ pis = sig0headmart(itypi,itypj)
+ eps_head = epsheadmart(itypi,itypj)
+!c!-------------------------------------------------------------------
+!c! R2 - distance between head of jth side chain and tail of ith sidechain
+ R2 = 0.0d0
+ DO k = 1, 3
+!c! Calculate head-to-tail distances
+ R2=R2+(chead(k,2)-ctail(k,1))**2
+ END DO
+!c! Pitagoras
+ R2 = dsqrt(R2)
+
+!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
+! write(iout,*) "KURWA2",Rhead
+ sparrow = w1 * Qj * om1
+ hawk = w2 * Qj * Qj * (1.0d0 - sqom2)
+ ECL = sparrow / Rhead**2.0d0 &
+ - hawk / Rhead**4.0d0
+!c!-------------------------------------------------------------------
+!c! derivative of ecl is Gcl
+!c! dF/dr part
+ dGCLdR =( - 2.0d0 * sparrow / Rhead**3.0d0 &
+ + 4.0d0 * hawk / Rhead**5.0d0)*sss_ele_cut
+!c! dF/dom1
+ dGCLdOM1 = (w1 * Qj) / (Rhead**2.0d0)
+!c! dF/dom2
+ dGCLdOM2 = (2.0d0 * w2 * Qj * Qj * om2) / (Rhead ** 4.0d0)
+!c--------------------------------------------------------------------
+!c--------------------------------------------------------------------
+!c Polarization energy
+!c Epol
+ MomoFac2 = (1.0d0 - chi2 * sqom1)
+ RR2 = R2 * R2 / MomoFac2
+ ee2 = exp(-(RR2 / (4.0d0 * a12sq)))
+ fgb2 = sqrt(RR2 + a12sq * ee2)
+ epol = 332.0d0 * eps_inout_fac * ((alphapol2/fgb2) ** 4.0d0 )
+ dPOLdFGB2 = -(1328.0d0 * eps_inout_fac * alphapol2 ** 4.0d0) &
+ / (fgb2 ** 5.0d0)
+ dFGBdR2 = ( (R2 / 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*sss_ele_cut
+!c! dPOLdR2 = 0.0d0
+ dPOLdOM1 = dPOLdFGB2 * dFGBdOM1
+!c! dPOLdOM1 = 0.0d0
+ dPOLdOM2 = 0.0d0
+!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 &
+ * (((-12.0d0*pis**12.0d0)/(Rhead**13.0d0)) &
+ + (( 6.0d0*pis**6.0d0) /(Rhead**7.0d0)))*sss_ele_cut
+!c!-------------------------------------------------------------------
+
+!c! Return the results
+!c! (see comments in Eqq)
+ DO k = 1, 3
+ erhead(k) = Rhead_distance(k)/Rhead
+ erhead_tail(k,2) = ((chead(k,2)-ctail(k,1))/R2)
+ END DO
+ erdxi = scalar( erhead(1), dC_norm(1,i+nres) )
+ erdxj = scalar( erhead(1), dC_norm(1,j) )
+ eagle = scalar( erhead_tail(1,2), dC_norm(1,j) )
+ adler = scalar( erhead_tail(1,2), dC_norm(1,i+nres) )
+ facd1 = d1 * vbld_inv(i+nres)
+ facd2 = d2 * vbld_inv(j)
+ facd3 = dtailmart(1,itypi,itypj) * vbld_inv(i+nres)
+ DO k = 1, 3
+ condor = (erhead_tail(k,2) &
+ + facd2 * (erhead_tail(k,2) - eagle * dC_norm(k,j)))
+
+ pom = erhead(k)+facd1*(erhead(k)-erdxi*dC_norm(k,i+nres))
+ gradpepmartx(k,i) = gradpepmartx(k,i) &
+ - dGCLdR * pom &
+ - dPOLdR2 * (erhead_tail(k,2) &
+ -facd3 * (erhead_tail(k,2) - adler * dC_norm(k,i+nres))) &
+ - dGLJdR * pom&
+ -(Ecl+Elj+Epol)*sss_ele_grad*rreal(k)*rij
+
+
+ pom = erhead(k)+facd2*(erhead(k)-erdxj*dC_norm(k,j))
+! gradpepmartx(k,j) = gradpepmartx(k,j) &
+! + dGCLdR * pom &
+! + dPOLdR2 * condor &
+! + dGLJdR * pom
+
+
+ gradpepmart(k,i) = gradpepmart(k,i) &
+ - dGCLdR * erhead(k) &
+ - dPOLdR2 * erhead_tail(k,2) &
+ - dGLJdR * erhead(k)&
+ -(Ecl+Elj+Epol)*sss_ele_grad*rreal(k)*rij
+
+
+ gradpepmart(k,j) = gradpepmart(k,j) &
+ + dGCLdR * erhead(k) &
+ + dPOLdR2 * erhead_tail(k,2) &
+ + dGLJdR * erhead(k)&
+ +(Ecl+Elj+Epol)*sss_ele_grad*rreal(k)*rij
+
+ END DO
+ RETURN
+ END SUBROUTINE edq_mart
+
+ SUBROUTINE edq_mart_pep(Ecl,Elj,Epol)
+ use comm_momo
+ use calc_data
+
+ double precision facd3, adler,ecl,elj,epol
+ alphapol2 = alphapolmart(itypi,itypj)
+ w1 = wqdipmart(1,itypi,itypj)
+ w2 = wqdipmart(2,itypi,itypj)
+ pis = sig0headmart(itypi,itypj)
+ eps_head = epsheadmart(itypi,itypj)
+!c!-------------------------------------------------------------------
+!c! R2 - distance between head of jth side chain and tail of ith sidechain
+ R2 = 0.0d0
+ DO k = 1, 3
+!c! Calculate head-to-tail distances
+ R2=R2+(chead(k,2)-ctail(k,1))**2
+ END DO
+!c! Pitagoras
+ R2 = dsqrt(R2)
+
+!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 * Qj * om1
+ hawk = w2 * Qj * Qj * (1.0d0 - sqom2)
+! print *,"CO2", itypi,itypj
+! print *,"CO?!.", w1,w2,Qj,om1
+ ECL = sparrow / Rhead**2.0d0 &
+ - hawk / Rhead**4.0d0
+!c!-------------------------------------------------------------------
+!c! derivative of ecl is Gcl
+!c! dF/dr part
+ dGCLdR = (- 2.0d0 * sparrow / Rhead**3.0d0 &
+ + 4.0d0 * hawk / Rhead**5.0d0)*sss_ele_cut
+!c! dF/dom1
+ dGCLdOM1 = (w1 * Qj) / (Rhead**2.0d0)
+!c! dF/dom2
+ dGCLdOM2 = (2.0d0 * w2 * Qj * Qj * om2) / (Rhead ** 4.0d0)
+!c--------------------------------------------------------------------
+!c--------------------------------------------------------------------
+!c Polarization energy
+!c Epol
+ MomoFac2 = (1.0d0 - chi2 * sqom1)
+ RR2 = R2 * R2 / MomoFac2
+ ee2 = exp(-(RR2 / (4.0d0 * a12sq)))
+ fgb2 = sqrt(RR2 + a12sq * ee2)
+ epol = 332.0d0 * eps_inout_fac * ((alphapol2/fgb2) ** 4.0d0 )
+ dPOLdFGB2 = -(1328.0d0 * eps_inout_fac * alphapol2 ** 4.0d0) &
+ / (fgb2 ** 5.0d0)
+ dFGBdR2 = ( (R2 / 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*sss_ele_cut
+!c! dPOLdR2 = 0.0d0
+ dPOLdOM1 = dPOLdFGB2 * dFGBdOM1
+!c! dPOLdOM1 = 0.0d0
+ dPOLdOM2 = 0.0d0
+!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)))
+!c!-------------------------------------------------------------------
+
+!c! Return the results
+!c! (see comments in Eqq)
+ DO k = 1, 3
+ erhead(k) = Rhead_distance(k)/Rhead
+ erhead_tail(k,2) = ((chead(k,2)-ctail(k,1))/R2)
+ END DO
+ erdxi = scalar( erhead(1), dC_norm(1,i) )
+ facd1 = d1 * vbld_inv(i+1)
+ DO k = 1, 3
+ pom = facd1*(erhead(k)-erdxi*dC_norm(k,i))
+! gradpepmartx(k,i) = gradpepmartx(k,i) &
+! - dGCLdR * pom &
+! - dPOLdR2 * (erhead_tail(k,2) &
+! -facd3 * (erhead_tail(k,2) - adler * dC_norm(k,i+nres))) &
+! - dGLJdR * pom
+
+! pom = erhead(k)+facd2*(erhead(k)-erdxj*dC_norm(k,j))
+! gradpepmartx(k,j) = gradpepmartx(k,j) &
+! + dGCLdR * pom &
+! + dPOLdR2 * condor &
+! + dGLJdR * pom
+
+ gradpepmart(k,i) = gradpepmart(k,i)+pom*(dGCLdR+dGLJdR)
+ gradpepmart(k,i+1) = gradpepmart(k,i+1)-pom*(dGCLdR+dGLJdR)
+
+ gradpepmart(k,i) = gradpepmart(k,i) +0.5d0*( &
+ - dGCLdR * erhead(k) &
+ - dPOLdR2 * erhead_tail(k,2) &
+ - dGLJdR * erhead(k))&
+ -(Ecl+Elj+Epol)*sss_ele_grad*rreal(k)*rij
+ gradpepmart(k,i+1) = gradpepmart(k,i+1) +0.5d0*( &
+ - dGCLdR * erhead(k) &
+ - dPOLdR2 * erhead_tail(k,2) &
+ - dGLJdR * erhead(k))&
+ -(Ecl+Elj+Epol)*sss_ele_grad*rreal(k)*rij
+
+
+
+ gradpepmart(k,j) = gradpepmart(k,j) &
+ + dGCLdR * erhead(k) &
+ + dPOLdR2 * erhead_tail(k,2) &
+ + dGLJdR * erhead(k)&
+ +(Ecl+Elj+Epol)*sss_ele_grad*rreal(k)*rij
+
+
+ END DO
+ RETURN
+ END SUBROUTINE edq_mart_pep
+!--------------------------------------------------------------------------
+
+ SUBROUTINE edd_mart(ECL)
+! IMPLICIT NONE
+ use comm_momo
+ use calc_data
+
+ double precision ecl
+!c! csig = sigiso(itypi,itypj)
+ w1 = wqdipmart(1,itypi,itypj)
+ w2 = wqdipmart(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 simplifimartion
+ 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
+!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))
+ gradpepmartx(k,i) = gradpepmartx(k,i) - dGCLdR * pom&
+ -ecl*sss_ele_grad*rij*rreal(k)
+! pom = erhead(k)+facd2*(erhead(k)-erdxj*dC_norm(k,j+nres))
+! gradpepmartx(k,j) = gradpepmartx(k,j) + dGCLdR * pom
+
+ gradpepmart(k,i) = gradpepmart(k,i) - dGCLdR * erhead(k)&
+ -ecl*sss_ele_grad*rij*rreal(k)
+
+ gradpepmart(k,j) = gradpepmart(k,j) + dGCLdR * erhead(k)&
+ +ecl*sss_ele_grad*rij*rreal(k)
+
+ END DO
+ RETURN
+ END SUBROUTINE edd_mart
+ SUBROUTINE edd_mart_pep(ECL)
+! IMPLICIT NONE
+ use comm_momo
+ use calc_data
+
+ double precision ecl
+!c! csig = sigiso(itypi,itypj)
+ w1 = wqdipmart(1,itypi,itypj)
+ w2 = wqdipmart(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
+!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))
+ gradpepmart(k,i) = gradpepmart(k,i) + dGCLdR * pom
+ gradpepmart(k,i+1) = gradpepmart(k,i+1) - dGCLdR * pom
+! pom = erhead(k)+facd2*(erhead(k)-erdxj*dC_norm(k,j+nres))
+! gradpepmartx(k,j) = gradpepmartx(k,j) + dGCLdR * pom
+
+ gradpepmart(k,i) = gradpepmart(k,i) - dGCLdR * erhead(k)*0.5d0&
+ -ECL*sss_ele_grad*rreal(k)*rij
+ gradpepmart(k,i+1) = gradpepmart(k,i+1)- dGCLdR * erhead(k)*0.5d0&
+ -ECL*sss_ele_grad*rreal(k)*rij
+
+ gradpepmart(k,j) = gradpepmart(k,j) + dGCLdR * erhead(k)&
+ +ECL*sss_ele_grad*rreal(k)*rij
+
+ END DO
+ RETURN
+ END SUBROUTINE edd_mart_pep
+
+ SUBROUTINE elgrad_init_mart(eheadtail,Egb,Ecl,Elj,Equad,Epol)
+ use comm_momo
+ use calc_data
+ real(kind=8) :: eheadtail,Egb,Ecl,Elj,Equad,Epol,Rb
+ eps_out=80.0d0
+ itypi = itype(i,1)
+ itypj = itype(j,4)
+! print *,"in elegrad",i,j,itypi,itypj
+!c! 1/(Gas Constant * Thermostate temperature) = BetaT
+!c! ENABLE THIS LINE WHEN USING CHECKGRAD!!!
+!c! t_bath = 300
+!c! BetaT = 1.0d0 / (t_bath * Rb)i
+ Rb=0.001986d0
+ BetaT = 1.0d0 / (298.0d0 * Rb)
+!c! Gay-berne var's
+ sig0ij = sigmamart( itypi,itypj )
+ chi1 = chi1mart( itypi, itypj )
+ chi2 = 0.0d0
+ chi12 = 0.0d0
+ chip1 = chipp1mart( itypi, itypj )
+ chip2 = 0.0d0
+ chip12 = 0.0d0
+!c! not used by momo potential, but needed by sc_angular which is shared
+!c! by all energy_potential subroutines
+ alf1 = 0.0d0
+ alf2 = 0.0d0
+ alf12 = 0.0d0
+ dxj = 0.0d0 !dc_norm( 1, nres+j )
+ dyj = 0.0d0 !dc_norm( 2, nres+j )
+ dzj = 0.0d0 !dc_norm( 3, nres+j )
+! print *,"before dheadmart"
+!c! distance from center of chain(?) to polar/charged head
+ d1 = dheadmart(1, 1, itypi, itypj)
+ d2 = dheadmart(2, 1, itypi, itypj)
+!c! ai*aj from Fgb
+ a12sq = rborn1mart(itypi,itypj) * rborn2mart(itypi,itypj)
+!c! a12sq = a12sq * a12sq
+!c! charge of amino acid itypi is...
+! print *,"after dheadmart"
+ Qi = icharge(itypi)
+ Qj = ichargelipid(itypj)
+ Qij = Qi * Qj
+! print *,"after icharge"
+
+!c! chis1,2,12
+ chis1 = chis1mart(itypi,itypj)
+ chis2 = 0.0d0
+ chis12 = 0.0d0
+ sig1 = sigmap1mart(itypi,itypj)
+ sig2 = sigmap2mart(itypi,itypj)
+! print *,"before alphasurmart"
+!c! alpha factors from Fcav/Gcav
+ b1cav = alphasurmart(1,itypi,itypj)
+ b2cav = alphasurmart(2,itypi,itypj)
+ b3cav = alphasurmart(3,itypi,itypj)
+ b4cav = alphasurmart(4,itypi,itypj)
+ wqd = wquadmart(itypi, itypj)
+! print *,"after alphasurmar n wquad"
+!c! used by Fgb
+ eps_in = epsintabmart(itypi,itypj)
+ eps_inout_fac = ( (1.0d0/eps_in) - (1.0d0/eps_out))
+!c!-------------------------------------------------------------------
+!c! tail lomartion and distance calculations
+ Rtail = 0.0d0
+ DO k = 1, 3
+ ctail(k,1)=c(k,i+nres)-dtailmart(1,itypi,itypj)*dc_norm(k,nres+i)
+ ctail(k,2)=c(k,j)!-dtailmart(2,itypi,itypj)*dc_norm(k,nres+j)
+ END DO
+!c! tail distances will be themselves usefull elswhere
+!c1 (in Gcav, for example)
+ Rtail_distance(1) = ctail( 1, 2 ) - ctail( 1,1 )
+ Rtail_distance(2) = ctail( 2, 2 ) - ctail( 2,1 )
+ Rtail_distance(3) = ctail( 3, 2 ) - ctail( 3,1 )
+ Rtail = dsqrt( &
+ (Rtail_distance(1)*Rtail_distance(1)) &
+ + (Rtail_distance(2)*Rtail_distance(2)) &
+ + (Rtail_distance(3)*Rtail_distance(3)))
+!c!-------------------------------------------------------------------
+!c! Calculate lomartion and distance between polar heads
+!c! distance between heads
+!c! for each one of our three dimensional space...
+ d1 = dheadmart(1, 1, itypi, itypj)
+ d2 = dheadmart(2, 1, itypi, itypj)
+
+ DO k = 1,3
+!c! lomartion of polar head is computed by taking hydrophobic centre
+!c! and moving by a d1 * dc_norm vector
+!c! see unres publimartions for very informative images
+ chead(k,1) = c(k, i+nres) + d1 * dc_norm(k, i+nres)
+ chead(k,2) = c(k, j)
+!c! distance
+!c! Rsc_distance(k) = dabs(c(k, i+nres) - c(k, j+nres))
+!c! Rsc(k) = Rsc_distance(k) * Rsc_distance(k)
+ Rhead_distance(k) = chead(k,2) - chead(k,1)
+ END DO
+!c! pitagoras (root of sum of squares)
+ Rhead = dsqrt( &
+ (Rhead_distance(1)*Rhead_distance(1)) &
+ + (Rhead_distance(2)*Rhead_distance(2)) &
+ + (Rhead_distance(3)*Rhead_distance(3)))
+!c!-------------------------------------------------------------------
+!c! zero everything that should be zero'ed
+ Egb = 0.0d0
+ ECL = 0.0d0
+ Elj = 0.0d0
+ Equad = 0.0d0
+ Epol = 0.0d0
+ eheadtail = 0.0d0
+ dGCLdOM1 = 0.0d0
+ dGCLdOM2 = 0.0d0
+ dGCLdOM12 = 0.0d0
+ dPOLdOM1 = 0.0d0
+ dPOLdOM2 = 0.0d0
+ RETURN
+ END SUBROUTINE elgrad_init_mart
+
+ SUBROUTINE elgrad_init_mart_pep(eheadtail,Egb,Ecl,Elj,Equad,Epol)
+ use comm_momo
+ use calc_data
+ real(kind=8) :: eheadtail,Egb,Ecl,Elj,Equad,Epol,Rb
+ eps_out=80.0d0
+ itypi = 10
+ itypj = itype(j,4)
+!c! 1/(Gas Constant * Thermostate temperature) = BetaT
+!c! ENABLE THIS LINE WHEN USING CHECKGRAD!!!
+!c! t_bath = 300
+!c! BetaT = 1.0d0 / (t_bath * Rb)i
+ Rb=0.001986d0
+ BetaT = 1.0d0 / (298.0d0 * Rb)
+!c! Gay-berne var's
+ sig0ij = sigmamart( itypi,itypj )
+ chi1 = chi1mart( itypi, itypj )
+ chi2 = 0.0d0
+ chi12 = 0.0d0
+ chip1 = chipp1mart( itypi, itypj )
+ chip2 = 0.0d0
+ chip12 = 0.0d0
+!c! not used by momo potential, but needed by sc_angular which is shared
+!c! by all energy_potential subroutines
+ alf1 = 0.0d0
+ alf2 = 0.0d0
+ alf12 = 0.0d0
+ dxj = 0.0d0 !dc_norm( 1, nres+j )
+ dyj = 0.0d0 !dc_norm( 2, nres+j )
+ dzj = 0.0d0 !dc_norm( 3, nres+j )
+!c! distance from center of chain(?) to polar/charged head
+ d1 = dheadmart(1, 1, itypi, itypj)
+ d2 = dheadmart(2, 1, itypi, itypj)
+!c! ai*aj from Fgb
+ a12sq = rborn1mart(itypi,itypj) * rborn2mart(itypi,itypj)
+!c! a12sq = a12sq * a12sq
+!c! charge of amino acid itypi is...
+ Qi = 0
+ Qj = ichargelipid(itypj)
+! Qij = Qi * Qj
+!c! chis1,2,12
+ chis1 = chis1mart(itypi,itypj)
+ chis2 = 0.0d0
+ chis12 = 0.0d0
+ sig1 = sigmap1mart(itypi,itypj)
+ sig2 = sigmap2mart(itypi,itypj)
+!c! alpha factors from Fcav/Gcav
+ b1cav = alphasurmart(1,itypi,itypj)
+ b2cav = alphasurmart(2,itypi,itypj)
+ b3cav = alphasurmart(3,itypi,itypj)
+ b4cav = alphasurmart(4,itypi,itypj)
+ wqd = wquadmart(itypi, itypj)
+!c! used by Fgb
+ eps_in = epsintabmart(itypi,itypj)
+ eps_inout_fac = ( (1.0d0/eps_in) - (1.0d0/eps_out))
+!c!-------------------------------------------------------------------
+!c! tail lomartion and distance calculations
+ Rtail = 0.0d0
+ DO k = 1, 3
+ ctail(k,1)=(c(k,i)+c(k,i+1))/2.0-dtailmart(1,itypi,itypj)*dc_norm(k,i)
+ ctail(k,2)=c(k,j)!-dtailmart(2,itypi,itypj)*dc_norm(k,nres+j)
+ END DO
+!c! tail distances will be themselves usefull elswhere
+!c1 (in Gcav, for example)
+ Rtail_distance(1) = ctail( 1, 2 ) - ctail( 1,1 )
+ Rtail_distance(2) = ctail( 2, 2 ) - ctail( 2,1 )
+ Rtail_distance(3) = ctail( 3, 2 ) - ctail( 3,1 )
+ Rtail = dsqrt( &
+ (Rtail_distance(1)*Rtail_distance(1)) &
+ + (Rtail_distance(2)*Rtail_distance(2)) &
+ + (Rtail_distance(3)*Rtail_distance(3)))
+!c!-------------------------------------------------------------------
+!c! Calculate lomartion and distance between polar heads
+!c! distance between heads
+!c! for each one of our three dimensional space...
+ d1 = dheadmart(1, 1, itypi, itypj)
+ d2 = dheadmart(2, 1, itypi, itypj)
+
+ DO k = 1,3
+!c! lomartion of polar head is computed by taking hydrophobic centre
+!c! and moving by a d1 * dc_norm vector
+!c! see unres publimartions for very informative images
+ chead(k,1) = (c(k, i)+c(k,i+1))/2.0 + d1 * dc_norm(k, i)
+ chead(k,2) = c(k, j)
+!c! distance
+!c! Rsc_distance(k) = dabs(c(k, i+nres) - c(k, j+nres))
+!c! Rsc(k) = Rsc_distance(k) * Rsc_distance(k)
+ Rhead_distance(k) = chead(k,2) - chead(k,1)
+ END DO
+!c! pitagoras (root of sum of squares)
+ Rhead = dsqrt( &
+ (Rhead_distance(1)*Rhead_distance(1)) &
+ + (Rhead_distance(2)*Rhead_distance(2)) &
+ + (Rhead_distance(3)*Rhead_distance(3)))
+!c!-------------------------------------------------------------------
+!c! zero everything that should be zero'ed
+ Egb = 0.0d0
+ ECL = 0.0d0
+ Elj = 0.0d0
+ Equad = 0.0d0
+ Epol = 0.0d0
+ eheadtail = 0.0d0
+ dGCLdOM1 = 0.0d0
+ dGCLdOM2 = 0.0d0
+ dGCLdOM12 = 0.0d0
+ dPOLdOM1 = 0.0d0
+ dPOLdOM2 = 0.0d0
+ RETURN
+ END SUBROUTINE elgrad_init_mart_pep
+
+ subroutine sc_grad_mart
+ use calc_data
+ real(kind=8), dimension(3) :: dcosom1,dcosom2
+ eom1=eps2der*eps2rt_om1-2.0D0*alf1*eps3der+sigder*sigsq_om1 &
+ +dCAVdOM1+ dGCLdOM1+ dPOLdOM1
+ eom2=eps2der*eps2rt_om2+2.0D0*alf2*eps3der+sigder*sigsq_om2 &
+ +dCAVdOM2+ dGCLdOM2+ dPOLdOM2
+
+ eom12=evdwij*eps1_om12+eps2der*eps2rt_om12 &
+ -2.0D0*alf12*eps3der+sigder*sigsq_om12&
+ +dCAVdOM12+ dGCLdOM12
+! diagnostics only
+! eom1=0.0d0
+! eom2=0.0d0
+! eom12=evdwij*eps1_om12
+! end diagnostics
+
+ do k=1,3
+ dcosom1(k)=rij*(dc_norm(k,nres+i)-om1*erij(k))
+ dcosom2(k)=rij*(dc_norm(k,j)-om2*erij(k))
+ enddo
+ do k=1,3
+ gg(k)=(gg(k)+eom1*dcosom1(k)+eom2*dcosom2(k))
+! print *,'gg',k,gg(k)
+ enddo
+! print *,i,j,gg_lipi(3),gg_lipj(3),sss_ele_cut
+! write (iout,*) "gg",(gg(k),k=1,3)
+ do k=1,3
+ gradpepmartx(k,i)=gradpepmartx(k,i)-gg(k)*sss_ele_cut &
+ +(eom12*(dc_norm(k,j)-om12*dc_norm(k,nres+i)) &
+ +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)) &
+! +eom2*(erij(k)-om2*dc_norm(k,j)))*dscj_inv
+
+! write (iout,*)(eom12*(dc_norm(k,nres+j)-om12*dc_norm(k,nres+i)) &
+! +eom1*(erij(k)-om1*dc_norm(k,nres+i)))*dsci_inv
+! write (iout,*)(eom12*(dc_norm(k,nres+i)-om12*dc_norm(k,nres+j)) &
+! +eom2*(erij(k)-om2*dc_norm(k,nres+j)))*dscj_inv
+ enddo
+!
+! Calculate the components of the gradient in DC and X
+!
+ do l=1,3
+ gradpepmart(l,i)=gradpepmart(l,i)-gg(l)*sss_ele_cut
+ gradpepmart(l,j)=gradpepmart(l,j)+gg(l)*sss_ele_cut
+ enddo
+ end subroutine sc_grad_mart
+
+ subroutine sc_grad_mart_pep
+ use calc_data
+ real(kind=8), dimension(3) :: dcosom1,dcosom2
+ eom1=eps2der*eps2rt_om1-2.0D0*alf1*eps3der+sigder*sigsq_om1 &
+ +dCAVdOM1+ dGCLdOM1+ dPOLdOM1
+ eom2=eps2der*eps2rt_om2+2.0D0*alf2*eps3der+sigder*sigsq_om2 &
+ +dCAVdOM2+ dGCLdOM2+ dPOLdOM2
+
+ eom12=evdwij*eps1_om12+eps2der*eps2rt_om12 &
+ -2.0D0*alf12*eps3der+sigder*sigsq_om12&
+ +dCAVdOM12+ dGCLdOM12
+! diagnostics only
+! eom1=0.0d0
+! 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)
+ gradpepmart(k,i)= gradpepmart(k,i) +sss_ele_cut*(0.5*(- gg(k)) &
+ + (-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)
+ gradpepmart(k,i+1)= gradpepmart(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 &
+ + (eom1*(erij(k)-om1*dc_norm(k,i)))*dsci_inv*2.0)
+ gradpepmart(k,j)=gradpepmart(k,j)+gg(k)*sss_ele_cut
+ enddo
+ end subroutine sc_grad_mart_pep
end module energy