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+ 0.44442019 0.21261136 4.10110530 2.6 asn phe
+ 0.49499497 0.11891284 3.55147963 3.1 asn ile
+ 0.53576677 0.15090652 3.71732693 2.8 asn leu
+ 0.52751327 0.11911315 3.51658941 3.1 asn val
+ 0.52684562 0.21607903 3.16744534 4.5 asn trp
+ 0.57007352 0.24209638 3.33886112 3.6 asn tyr
+ 0.53360274 0.10469691 3.77047757 2.1 asn ala
+ 0.53096441 0.17749158 3.52240926 2.4 asn gly
+ 0.40760213 0.22182945 3.87932811 2.9 asn thr
+ 0.47722200 0.11590346 3.72665420 2.4 asn ser
+ 0.43939620 0.14592084 3.33545255 3.7 asn gln
+ 0.46547953 0.08929379 3.07503648 4.2 asn asn
+ 0.45066424 0.03916198 3.88381092 2.6 asn glu
+ 0.56591130 0.16761648 3.73937544 2.6 asn asp
+ 0.53142890 0.30777945 3.38670300 3.4 asn his
+ 0.30442390 0.01364112 4.48141529 1.9 asn arg
+ 0.27593110 0.18004212 4.18933053 2.5 asn lys
+ 0.50353752 0.32164896 3.73467727 2.9 asn pro
+ 0.44333739 0.28309684 4.06717512 2.5 asn sme
+ 0.44442019 0.21261136 4.10110530 2.6 asn dbz
+ 0.53360274 0.10469691 3.77047757 2.1 asn aib
+ 0.53360274 0.10469691 3.77047757 2.1 asn abu
+ 0.45167162 0.28718023 3.99873956 2.0 glu cys
+ 0.58329544 0.31669128 3.41282057 3.5 glu met
+ 0.65649724 0.21234517 3.93827274 2.7 glu phe
+ 0.53672118 0.18971451 3.82344372 3.1 glu ile
+ 0.61529042 0.23787159 4.40927943 1.8 glu leu
+ 0.57711221 0.16371932 4.06702052 2.5 glu val
+ 0.57842612 0.14725703 3.09551785 4.5 glu trp
+ 0.68045805 0.20875844 3.42836329 3.5 glu tyr
+ 0.52828434 0.09169166 3.50057256 2.6 glu ala
+ 0.54349648 0.27262886 3.90940249 1.9 glu gly
+ 0.65080974 0.43402569 3.91402729 2.8 glu thr
+ 0.47242896 0.07323090 4.61451625 1.5 glu ser
+ 0.45962325 0.34422613 3.53114474 3.5 glu gln
+ 0.45784628 0.08542837 3.88381092 2.6 glu asn
+ 0.45136983 0.32035022 3.77778958 2.9 glu glu
+ 0.40995790 -0.03116378 4.26798075 2.0 glu asp
+ 0.52859120 0.16354546 3.78696151 3.1 glu his
+ 0.55740234 0.22045560 3.81136201 3.1 glu arg
+ 0.55181260 0.35744091 4.66520100 1.6 glu lys
+ 0.66236078 0.36052823 3.47970840 3.3 glu pro
+ 0.58329544 0.31669128 3.41282057 3.5 glu sme
+ 0.65649724 0.21234517 3.93827274 2.7 glu dbz
+ 0.52828434 0.09169166 3.50057256 2.6 glu aib
+ 0.52828434 0.09169166 3.50057256 2.6 glu abu
+ 0.32481843 0.30241943 3.42940555 3.0 asp cys
+ 0.48146154 0.12184204 3.94820588 2.2 asp met
+ 0.49531096 0.13459205 4.16332864 2.3 asp phe
+ 0.48629858 0.10892335 4.20071886 2.1 asp ile
+ 0.42458969 0.04067298 4.12366306 2.3 asp leu
+ 0.46012374 0.06388031 4.12654645 2.1 asp val
+ 0.44400377 0.21493328 3.56336594 3.9 asp trp
+ 0.49469528 0.08857244 3.25938544 4.0 asp tyr
+ 0.43791837 0.09152666 3.56513816 2.4 asp ala
+ 0.40782681 0.10505865 3.87388976 1.8 asp gly
+ 0.53260595 0.06977694 3.89588321 2.3 asp thr
+ 0.41899901 0.06697791 3.72754795 2.4 asp ser
+ 0.31470323 0.16090621 4.15342990 2.3 asp gln
+ 0.41087617 0.03408678 3.73937544 2.6 asp asn
+ 0.36889970 -0.15930847 4.26798075 2.0 asp glu
+ 0.49914534 0.28237257 3.82849221 2.6 asp asp
+ 0.35831041 0.17803592 3.53238450 3.3 asp his
+ 0.46844169 0.00518452 2.71889129 5.3 asp arg
+ 0.33974035 0.00746795 4.11707156 2.3 asp lys
+ 0.58065436 0.12893457 3.46466683 2.9 asp pro
+ 0.48146154 0.12184204 3.94820588 2.2 asp sme
+ 0.49531096 0.13459205 4.16332864 2.3 asp dbz
+ 0.43791837 0.09152666 3.56513816 2.4 asp aib
+ 0.43791837 0.09152666 3.56513816 2.4 asp abu
+ 0.66712991 -0.00059312 3.45279388 2.8 his cys
+ 0.62023666 0.07810136 3.67829283 2.8 his met
+ 0.54813450 0.02387399 3.97249455 2.6 his phe
+ 0.50448776 0.10129703 3.87438904 3.0 his ile
+ 0.43502367 -0.13271534 3.48566489 3.5 his leu
+ 0.50083039 0.09390639 4.17589586 2.4 his val
+ 0.34876524 0.17810403 3.41608597 4.4 his trp
+ 0.52214146 -0.08932064 4.02269765 2.4 his tyr
+ 0.62795477 -0.02594442 3.19268981 2.9 his ala
+ 0.55372190 0.05824969 3.23796583 3.0 his gly
+ 0.41891546 0.11138432 4.11716100 2.7 his thr
+ 0.54068082 -0.04376077 3.18728475 3.7 his ser
+ 0.52837481 -0.09497389 3.09986815 4.1 his gln
+ 0.59926199 -0.09807584 3.38670300 3.4 his asn
+ 0.30784556 -0.28464757 3.78696151 3.1 his glu
+ 0.57435087 0.02111146 3.53238450 3.3 his asp
+ 0.65809056 -0.09152492 2.98047276 4.0 his his
+ 0.54935375 -0.06444900 3.84130645 3.2 his arg
+ 0.55747594 0.18348617 4.00467347 2.6 his lys
+ 0.61284214 0.16197710 3.89481022 2.5 his pro
+ 0.62023666 0.07810136 3.67829283 2.8 his sme
+ 0.54813450 0.02387399 3.97249455 2.6 his dbz
+ 0.62795477 -0.02594442 3.19268981 2.9 his aib
+ 0.62795477 -0.02594442 3.19268981 2.9 his abu
+ 0.75225350 0.20735450 3.53908504 2.8 arg cys
+ 0.61621105 0.32748378 3.92004157 3.0 arg met
+ 0.66251194 0.14629924 3.92791573 3.4 arg phe
+ 0.57629387 0.00597023 4.27655600 2.9 arg ile
+ 0.74108830 0.24297317 3.53775960 3.6 arg leu
+ 0.62859689 0.04738249 4.00988606 3.0 arg val
+ 0.76107791 0.21620637 3.01681706 5.0 arg trp
+ 0.64334219 -0.01420347 3.36685862 4.3 arg tyr
+ 0.61765505 -0.23266856 4.09477647 1.9 arg ala
+ 0.63577289 0.03826170 3.25922115 3.2 arg gly
+ 0.52962288 0.04658043 4.12871646 2.8 arg thr
+ 0.57322475 -0.01630823 3.87794402 2.5 arg ser
+ 0.63768385 -0.04885203 3.59510761 3.4 arg gln
+ 0.60938603 0.03300984 4.48141529 1.9 arg asn
+ 0.63351724 -0.10980006 3.81136201 3.1 arg glu
+ 0.63619125 -0.04461328 2.71889129 5.3 arg asp
+ 0.61095825 0.10189057 3.84130645 3.2 arg his
+ 0.71730775 0.08728438 2.81437659 5.4 arg arg
+ 0.60658407 -0.03333816 4.23716346 2.5 arg lys
+ 0.68568576 0.07786298 3.77385723 3.0 arg pro
+ 0.61621105 0.32748378 3.92004157 3.0 arg sme
+ 0.66251194 0.14629924 3.92791573 3.4 arg dbz
+ 0.61765505 -0.23266856 4.09477647 1.9 arg aib
+ 0.61765505 -0.23266856 4.09477647 1.9 arg abu
+ 0.76470157 0.76084085 3.85035238 2.3 lys cys
+ 0.67255968 0.44875322 4.49980555 2.0 lys met
+ 0.76960024 0.60831176 3.95551322 3.0 lys phe
+ 0.61378093 0.26242515 4.52497861 1.8 lys ile
+ 0.71563444 0.68072580 4.36103401 2.2 lys leu
+ 0.67409525 0.58814366 4.64018900 2.0 lys val
+ 0.88671210 1.00380282 3.76243382 3.8 lys trp
+ 0.67158296 0.42635325 4.14326778 2.9 lys tyr
+ 0.67254432 0.35248523 4.42291744 0.9 lys ala
+ 0.69462202 0.31735268 4.01153241 1.5 lys gly
+ 0.58760205 0.22591520 5.19110983 0.8 lys thr
+ 0.62437605 0.35173136 4.37211026 1.5 lys ser
+ 0.70291910 0.54587675 4.40523407 1.8 lys gln
+ 0.71487329 0.62683782 4.18933053 2.5 lys asn
+ 0.63139916 0.33371478 4.66520100 1.6 lys glu
+ 0.72656677 0.46183912 4.11707156 2.3 lys asp
+ 0.83364969 0.89847717 4.00467347 2.6 lys his
+ 0.77862679 0.71215250 4.23716346 2.5 lys arg
+ 0.56582949 -0.04350298 4.78186650 1.3 lys lys
+ 0.80330046 0.84741487 4.53882609 2.0 lys pro
+ 0.67255968 0.44875322 4.49980555 2.0 lys sme
+ 0.76960024 0.60831176 3.95551322 3.0 lys dbz
+ 0.67254432 0.35248523 4.42291744 0.9 lys aib
+ 0.67254432 0.35248523 4.42291744 0.9 lys abu
+ 0.49304685 -0.20581200 3.62096650 1.9 pro cys
+ 0.12683702 -0.30939905 3.76955189 2.7 pro met
+ 0.11511445 -0.18829660 3.77053096 2.9 pro phe
+ 0.05125111 -0.18929142 4.93089469 1.5 pro ile
+ 0.11747631 -0.02693818 4.08852337 2.4 pro leu
+ 0.26952062 0.30671521 4.56454004 2.0 pro val
+ 0.38994700 -0.04061465 3.94460593 2.7 pro trp
+ 0.29377104 0.11826092 3.95285757 2.9 pro tyr
+ 0.25804259 -0.13915496 3.38612759 2.5 pro ala
+ 0.38094914 -0.14696919 3.41316198 2.1 pro gly
+ 0.30752420 0.17160109 3.81482913 2.9 pro thr
+ 0.07822398 0.05027273 4.22414116 2.0 pro ser
+ 0.14107113 -0.04129291 4.27763332 2.2 pro gln
+ 0.21471187 -0.00268809 3.73467727 2.9 pro asn
+ 0.22170637 -0.11224658 3.47970840 3.3 pro glu
+ 0.08872349 -0.40993001 3.46466683 2.9 pro asp
+ 0.31135187 0.03163507 3.89481022 2.5 pro his
+ 0.38918420 0.21697911 3.77385723 3.0 pro arg
+ -0.11536833 -0.12070488 4.53882609 2.0 pro lys
+ 0.24887782 -0.07176013 3.66640730 2.7 pro pro
+ 0.12683702 -0.30939905 3.76955189 2.7 pro sme
+ 0.11511445 -0.18829660 3.77053096 2.9 pro dbz
+ 0.25804259 -0.13915496 3.38612759 2.5 pro aib
+ 0.25804259 -0.13915496 3.38612759 2.5 pro abu
+ 0.68048894 -0.06899195 3.60729199 2.1 sme cys
+ 0.47168906 -0.01389221 3.62448254 3.4 sme met
+ 0.38809483 0.05839704 3.69650927 3.8 sme phe
+ 0.30403358 -0.17995008 4.29852296 2.5 sme ile
+ 0.33973020 -0.34834021 4.94950826 1.2 sme leu
+ 0.30071237 0.01285368 4.18347745 2.6 sme val
+ 0.52333332 0.17569346 3.51061576 4.2 sme trp
+ 0.61170525 0.20950877 4.06080648 3.0 sme tyr
+ 0.41902197 -0.08043824 3.17380260 3.3 sme ala
+ 0.52139540 0.00438353 3.43153041 2.6 sme gly
+ 0.49784550 0.12355497 4.19683352 2.2 sme thr
+ 0.63180941 -0.16149377 4.09465313 1.6 sme ser
+ 0.44886809 -0.15991724 3.53814108 3.3 sme gln
+ 0.41073744 0.00740397 4.06717512 2.5 sme asn
+ 0.54442625 -0.07267571 3.41282057 3.5 sme glu
+ 0.63996137 -0.06915184 3.94820588 2.2 sme asp
+ 0.62501187 0.11051556 3.67829283 2.8 sme his
+ 0.53066821 0.05034669 3.92004157 3.0 sme arg
+ 0.33560623 -0.08136851 4.49980555 2.0 sme lys
+ 0.49366704 -0.10767906 3.76955189 2.7 sme pro
+ 0.47168906 -0.01389221 3.62448254 3.4 sme sme
+ 0.38809483 0.05839704 3.69650927 3.8 sme dbz
+ 0.41902197 -0.08043824 3.17380260 3.3 sme aib
+ 0.41902197 -0.08043824 3.17380260 3.3 sme abu
+ 0.36262117 -0.19622749 4.17039421 2.4 dbz cys
+ 0.26128467 0.01513555 3.69650927 3.8 dbz met
+ 0.20490480 -0.09214195 4.22979013 3.0 dbz phe
+ 0.28320764 -0.11272094 4.28523432 2.8 dbz ile
+ 0.49776022 0.15233796 3.52640364 3.7 dbz leu
+ 0.38397299 0.13538890 4.83243966 2.0 dbz val
+ 0.37298546 -0.07130682 3.38863637 4.4 dbz trp
+ 0.50532840 -0.04912285 3.56784740 3.7 dbz tyr
+ 0.47086276 -0.20131132 3.61044593 2.4 dbz ala
+ 0.47136787 -0.02932642 3.89454305 2.0 dbz gly
+ 0.43636452 0.05389401 4.20612459 2.6 dbz thr
+ 0.39664510 0.04040127 3.97909758 2.6 dbz ser
+ 0.37270815 -0.11268458 3.88510036 3.0 dbz gln
+ 0.55039146 -0.03205935 4.10110530 2.6 dbz asn
+ 0.33746013 -0.24962819 3.93827274 2.7 dbz glu
+ 0.43948791 -0.14279533 4.16332864 2.3 dbz asp
+ 0.57384992 -0.03571288 3.97249455 2.6 dbz his
+ 0.49181945 0.18810757 3.92791573 3.4 dbz arg
+ 0.34273176 -0.21712089 3.95551322 3.0 dbz lys
+ 0.44953604 -0.00243978 3.77053096 2.9 dbz pro
+ 0.26128467 0.01513555 3.69650927 3.8 dbz sme
+ 0.20490480 -0.09214195 4.22979013 3.0 dbz dbz
+ 0.47086276 -0.20131132 3.61044593 2.4 dbz aib
+ 0.47086276 -0.20131132 3.61044593 2.4 dbz abu
+ 0.31170564 0.13087300 3.40011763 2.2 ala cys
+ 0.35817150 -0.05118436 3.17380260 3.3 ala met
+ 0.35531356 -0.07100358 3.61044593 2.4 ala phe
+ 0.16898670 0.06047415 3.66929044 2.7 ala ile
+ 0.29707520 -0.00251129 4.02083643 1.8 ala leu
+ 0.16009076 -0.19966586 4.10663351 1.7 ala val
+ 0.33543361 0.02729744 3.47226781 3.7 ala trp
+ 0.40771637 0.04944451 3.22022624 3.4 ala tyr
+ 0.32491593 0.00199416 3.48648915 1.4 ala ala
+ 0.32250163 0.00199416 3.50576712 1.1 ala gly
+ 0.44809712 -0.03625897 3.28319535 2.9 ala thr
+ 0.32570984 0.00199416 3.48018928 2.2 ala ser
+ 0.25708601 -0.02518611 3.98829105 2.0 ala gln
+ 0.27223871 0.02170282 3.77047757 2.1 ala asn
+ 0.37126794 -0.02710099 3.50057256 2.6 ala glu
+ 0.15955468 -0.05289865 3.56513816 2.4 ala asp
+ 0.41120950 0.04944451 3.19268981 2.9 ala his
+ 0.27446733 0.00786488 4.09477647 1.9 ala arg
+ 0.22981425 -0.09322596 4.42291744 0.9 ala lys
+ 0.37507388 0.05588781 3.38612759 2.5 ala pro
+ 0.35817150 -0.05118436 3.17380260 3.3 ala sme
+ 0.35531356 -0.07100358 3.61044593 2.4 ala dbz
+ 0.32491593 0.00199416 3.48648915 1.4 ala aib
+ 0.32491593 0.00199416 3.48648915 1.4 ala abu
+ 0.31170564 0.13087300 3.40011763 2.2 ala cys
+ 0.35817150 -0.05118436 3.17380260 3.3 ala met
+ 0.35531356 -0.07100358 3.61044593 2.4 ala phe
+ 0.16898670 0.06047415 3.66929044 2.7 ala ile
+ 0.29707520 -0.00251129 4.02083643 1.8 ala leu
+ 0.16009076 -0.19966586 4.10663351 1.7 ala val
+ 0.33543361 0.02729744 3.47226781 3.7 ala trp
+ 0.40771637 0.04944451 3.22022624 3.4 ala tyr
+ 0.32491593 0.00199416 3.48648915 1.4 ala ala
+ 0.32250163 0.00199416 3.50576712 1.1 ala gly
+ 0.44809712 -0.03625897 3.28319535 2.9 ala thr
+ 0.32570984 0.00199416 3.48018928 2.2 ala ser
+ 0.25708601 -0.02518611 3.98829105 2.0 ala gln
+ 0.27223871 0.02170282 3.77047757 2.1 ala asn
+ 0.37126794 -0.02710099 3.50057256 2.6 ala glu
+ 0.15955468 -0.05289865 3.56513816 2.4 ala asp
+ 0.41120950 0.04944451 3.19268981 2.9 ala his
+ 0.27446733 0.00786488 4.09477647 1.9 ala arg
+ 0.22981425 -0.09322596 4.42291744 0.9 ala lys
+ 0.37507388 0.05588781 3.38612759 2.5 ala pro
+ 0.35817150 -0.05118436 3.17380260 3.3 ala sme
+ 0.35531356 -0.07100358 3.61044593 2.4 ala dbz
+ 0.32491593 0.00199416 3.48648915 1.4 ala aib
+ 0.32491593 0.00199416 3.48648915 1.4 ala abu
elseif(UNRES_MD_FF STREQUAL "E0LL2Y")
# set preprocesor flags
set(CPPFLAGS "PROCOR -DSPLITELE -DSCCORPDB" )
+elseif(UNRES_MD_FF STREQUAL "NEWCORR")
+ # set preprocesor flags
+ set(CPPFLAGS "PROCOR -DUNRES -DISNAN -DSPLITELE -DLANG0 -DNEWCORR -DCORRCD" )
elseif(UNRES_MD_FF STREQUAL "4P")
set(CPPFLAGS "SPLITELE -DLANG0 -DCRYST_BOND -DCRYST_THETA -DCRYST_SC -DSCCORPDB" )
endif(UNRES_MD_FF STREQUAL "GAB")
c,cref
use energy_data, only: nnt,nct
use control_data, only: symetr,outpdb,outmol2,titel,&
- iopt,print_dist !,MaxProcs
+ iopt,print_dist,nclust !,MaxProcs
use control, only: tcpu,initialize
use wham_data, only: punch_dist
INTEGER,dimension(:),allocatable :: HVALS !(maxconf-1)
INTEGER,dimension(:),allocatable :: IORDER,HEIGHT !(maxconf-1)
integer,dimension(:),allocatable :: nn !(maxconf)
- integer :: ndis
+ integer :: ndis,is,ie
real(kind=4),dimension(:),allocatable :: DISNN !(maxconf)
LOGICAL,dimension(:),allocatable :: FLAG !(maxconf)
integer :: i,j,k,l,m,n,len,lev,idum,ii,ind,jj,icut,ncon,&
!elwrite(iout,*) "before parmread"
call openunits
!elwrite(iout,*) "before parmread"
- call parmread
call read_control
+ call parmread
+! call read_control
!elwrite(iout,*) "after read control"
call molread
! if (refstr) call read_ref_structure(*30)
! write (iout,*) "after permut"
! call flush(iout)
print *,'MAIN: nnt=',nnt,' nct=',nct
-
+ if (nclust.gt.0) then
+ PRINTANG(1)=.TRUE.
+ PRINTPDB(1)=outpdb
+ printmol2(1)=outmol2
+ ncut=0
+ else
DO I=1,NCUT
PRINTANG(I)=.FALSE.
PRINTPDB(I)=0
printmol2(i)=outmol2
ENDIF
ENDDO
+ endif
+ if (ncut.gt.0) then
write (iout,*) 'Number of cutoffs:',NCUT
write (iout,*) 'Cutoff values:'
DO ICUT=1,NCUT
WRITE(IOUT,'(8HRCUTOFF(,I2,2H)=,F8.1,2i2)')ICUT,RCUTOFF(ICUT),&
printpdb(icut),printmol2(icut)
ENDDO
+ else if (nclust.gt.0) then
+ write (iout,'("Number of clusters requested",i5)') nclust
+ else
+ if (me.eq.Master) &
+ write (iout,*) "ERROR: Either nclust or ncut must be >0"
+ stop
+ endif
DO I=1,NRES-3
MULT(I)=1
ENDDO
allocate(iass(maxgr))
allocate(nconf(maxgr,maxingr))
allocate(totfree_gr(maxgr))
-
+!c 3/3/16 AL: added explicit number of cluters
+ if (nclust.gt.0) then
+ is=nclust-1
+ ie=nclust-1
+ icut=1
+ else
+ is=1
+ ie=lev-1
+ endif
do i=1,maxgr
licz(i)=0
enddo
icut=1
- i=1
- NGR=i+1
+ i=is
+ NGR=is+1
do j=1,n
licz(iclass(j,i))=licz(iclass(j,i))+1
nconf(iclass(j,i),licz(iclass(j,i)))=j
! write (iout,*) i,j,iclass(j,i),licz(iclass(j,i)),
! & nconf(iclass(j,i),licz(iclass(j,i)))
enddo
- do i=1,lev-1
-
+! do i=1,lev-1
+ do i=is,ie
idum=lev-i
DO L=1,LEV
IF (HEIGHT(L).EQ.IDUM) GOTO 190
190 IDUM=L
write(IOUT,*) "i+1",i+1," idum",idum," critval",CRITVAL(IDUM),&
" icut",icut," cutoff",rcutoff(icut)
- IF (CRITVAL(IDUM).LT. RCUTOFF(ICUT)) THEN
+ IF (nclust.gt.0.or.CRITVAL(IDUM).LT. RCUTOFF(ICUT)) THEN
+ if (nclust.le.0) &
WRITE (iout,'(/a,f10.5)') 'AT CUTOFF:',rcutoff(icut)
write (iout,'(a,f8.2)') 'Maximum distance found:',&
CRITVAL(IDUM)
do l=1,maxgr
licz(l)=0
enddo
+ ii=i-is+1
do j=1,n
- enddo
- do j=1,n
- licz(iclass(j,i))=licz(iclass(j,i))+1
- nconf(iclass(j,i),licz(iclass(j,i)))=j
+ licz(iclass(j,ii))=licz(iclass(j,ii))+1
+ nconf(iclass(j,ii),licz(iclass(j,ii)))=j
!d write (iout,*) i,j,iclass(j,i),licz(iclass(j,i)),&
!d nconf(iclass(j,i),licz(iclass(j,i)))
!d print *,j,iclass(j,i),
use control_data, only: titel,outpdb,outmol2,refstr,pdbref,&
iscode,symetr,punch_dist,print_dist,nstart,nend,&
caonly,iopt,efree,lprint_cart,lprint_int,rlamb_ele,&
- r_cut_ele
+ r_cut_ele,nclust,tor_mode,scelemode
! implicit none
! include 'DIMENSIONS'
! include 'sizesclu.dat'
call reada(controlcard,'BOXX',boxxsize,100.0d0)
call reada(controlcard,'BOXY',boxysize,100.0d0)
call reada(controlcard,'BOXZ',boxzsize,100.0d0)
+ call readi(controlcard,'NCLUST',nclust,5)
! ions=index(controlcard,"IONS").gt.0
+ call readi(controlcard,"SCELEMODE",scelemode,0)
+ print *,"SCELE",scelemode
+ call readi(controlcard,'TORMODE',tor_mode,0)
+!C if(me.eq.king .or. .not. out1file .and. fg_rank.eq.0) then
+ write(iout,*) "torsional and valence angle mode",tor_mode
call reada(controlcard,"R_CUT_ELE",r_cut_ele,15.0d0)
call reada(controlcard,"LAMBDA_ELE",rlamb_ele,0.3d0)
write(iout,*) "R_CUT_ELE=",r_cut_ele
call initialize
call openunits
- call parmread
call read_control
+ call parmread
+! call read_control
call molread
c if (refstr) call read_ref_structure(*30)
do i=1,nres
c call flush(iout)
print *,'MAIN: nnt=',nnt,' nct=',nct
+ if (nclust.gt.0) then
+ PRINTANG(1)=.TRUE.
+ PRINTPDB(1)=outpdb
+ printmol2(1)=outmol2
+ ncut=0
+ else
DO I=1,NCUT
PRINTANG(I)=.FALSE.
PRINTPDB(I)=0
printmol2(i)=outmol2
ENDIF
ENDDO
+ endif
+ if (ncut.gt.0) then
write (iout,*) 'Number of cutoffs:',NCUT
write (iout,*) 'Cutoff values:'
DO ICUT=1,NCUT
WRITE(IOUT,'(8HRCUTOFF(,I2,2H)=,F8.1,2i2)')ICUT,RCUTOFF(ICUT),
& printpdb(icut),printmol2(icut)
ENDDO
+ else if (nclust.gt.0) then
+ write (iout,'("Number of clusters requested",i5)') nclust
+ else
+ if (me.eq.Master)
+ & write (iout,*) "ERROR: Either nclust or ncut must be >0"
+ stop
+ endif
DO I=1,NRES-3
MULT(I)=1
ENDDO
goto 192
endif
CALL HCASS(N,IA,IB,CRIT,LEV,ICLASS,HVALS,IORDER,CRITVAL,HEIGHT)
-c CALL HCDEN(LEV,IORDER,HEIGHT,CRITVAL)
+!c CALL HCDEN(LEV,IORDER,HEIGHT,CRITVAL)
+!c 3/3/16 AL: added explicit number of cluters
+ if (nclust.gt.0) then
+ is=nclust-1
+ ie=nclust-1
+ icut=1
+ else
+ is=1
+ ie=lev-1
+ endif
do i=1,maxgr
licz(i)=0
enddo
icut=1
- i=1
- NGR=i+1
+ i=is
+ NGR=is+1
do j=1,n
licz(iclass(j,i))=licz(iclass(j,i))+1
nconf(iclass(j,i),licz(iclass(j,i)))=j
-c write (iout,*) i,j,iclass(j,i),licz(iclass(j,i)),
-c & nconf(iclass(j,i),licz(iclass(j,i)))
+!c write (iout,*) i,j,iclass(j,i),licz(iclass(j,i)),
+!c & nconf(iclass(j,i),licz(iclass(j,i)))
enddo
do i=1,lev-1
190 IDUM=L
write(IOUT,*) "i+1",i+1," idum",idum," critval",CRITVAL(IDUM),
& " icut",icut," cutoff",rcutoff(icut)
- IF (CRITVAL(IDUM).LT. RCUTOFF(ICUT)) THEN
- WRITE (iout,'(/a,f10.5)') 'AT CUTOFF:',rcutoff(icut)
+ IF (nclust.gt.0.or.CRITVAL(IDUM).LT. RCUTOFF(ICUT)) THEN
+ if (nclust.le.0) WRITE (iout,'(/a,f10.5)') 'AT CUTOFF:',rcutoff(icut)
write (iout,'(a,f8.2)') 'Maximum distance found:',
& CRITVAL(IDUM)
CALL SRTCLUST(ICUT,ncon_work,iT)
gnorm_check,gradout,split_ene,with_theta_constr,protein,ions,nucleic,&
raw_psipred
#ifdef CLUSTER
- integer :: iopt,nend,nstart,outpdb,outmol2 !cluster
+ integer :: iopt,nend,nstart,outpdb,outmol2,nclust !cluster
logical :: punch_dist,print_dist,lside,lprint_cart,lprint_int,&
caonly,efree,from_bx,from_cx,from_cart ! cluster
#else
- module energy
+ module energy
!-----------------------------------------------------------------------------
use io_units
use names
call AFMforce(Eafmforce)
else if (selfguide.gt.0) then
call AFMvel(Eafmforce)
+ else
+ Eafmforce=0.0d0
endif
endif
if (tubemode.eq.1) then
eespp=0.0d0
endif
! write(iout,*) ecorr_nucl,"ecorr_nucl",nres_molec(2)
-! print *,"before ecatcat"
+! print *,"before ecatcat",wcatcat
if (nfgtasks.gt.1) then
if (fg_rank.eq.0) then
call ecatcat(ecationcation)
! Here are the energies showed per procesor if the are more processors
! per molecule then we sum it up in sum_energy subroutine
! print *," Processor",myrank," calls SUM_ENERGY"
- energia(41)=ecation_prot
- energia(42)=ecationcation
+ energia(42)=ecation_prot
+ energia(41)=ecationcation
energia(46)=escbase
energia(47)=epepbase
energia(48)=escpho
etors_d_nucl=energia(36)
ecorr_nucl=energia(37)
ecorr3_nucl=energia(38)
- ecation_prot=energia(41)
- ecationcation=energia(42)
+ ecation_prot=energia(42)
+ ecationcation=energia(41)
escbase=energia(46)
epepbase=energia(47)
escpho=energia(48)
etors_d_nucl=energia(36)
ecorr_nucl=energia(37)
ecorr3_nucl=energia(38)
- ecation_prot=energia(41)
- ecationcation=energia(42)
+ ecation_prot=energia(42)
+ ecationcation=energia(41)
escbase=energia(46)
epepbase=energia(47)
escpho=energia(48)
ecorr,wcorr,&
ecorr5,wcorr5,ecorr6,wcorr6,eel_loc,wel_loc,eello_turn3,wturn3,&
eello_turn4,wturn4,eello_turn6,wturn6,esccor,wsccor,edihcnstr,&
- ethetacnstr,ebr*nss,Uconst,eliptran,wliptran,Eafmforc, &
+ ethetacnstr,ebr*nss,Uconst,eliptran,wliptran,Eafmforce, &
etube,wtube, &
estr_nucl,wbond_nucl, ebe_nucl,wang_nucl,&
- evdwpp,wvdwpp_nucl,eespp,welpp,evdwpsb,wvdwpsb,eelpsb,welpsb&
- evdwsb,wvdwsb,eelsb,welsb,esbloc,wsbloc,etors_nucl,wtor_nucl&
+ evdwpp,wvdwpp_nucl,eespp,welpp,evdwpsb,wvdwpsb,eelpsb,welpsb,&
+ evdwsb,wvdwsb,eelsb,welsb,esbloc,wsbloc,etors_nucl,wtor_nucl,&
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,&
! write(iout,*)"c ", c(1,:), c(2,:), c(3,:)
rrij=1.0D0/(xj*xj+yj*yj+zj*zj)
rij=dsqrt(rrij)
- sss_ele_cut=sscale_ele(1.0d0/(rij*sigma(itypi,itypj)))
- sss_ele_grad=sscagrad_ele(1.0d0/(rij*sigma(itypi,itypj)))
+ 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
fac=rij*fac
! print *,'before fac',fac,rij,evdwij
fac=fac+evdwij*sss_ele_grad/sss_ele_cut&
- /sigma(itypi,itypj)*rij
+ *rij
! print *,'grad part scale',fac, &
! evdwij*sss_ele_grad/sss_ele_cut &
! /sigma(itypi,itypj)*rij
+wcorr3_nucl*gradcorr3_nucl(j,i) +&
wcatprot* gradpepcat(j,i)+ &
wcatcat*gradcatcat(j,i)+ &
- wscbase*gvdwc_scbase(j,i) &
+ wscbase*gvdwc_scbase(j,i)+ &
wpepbase*gvdwc_pepbase(j,i)+&
wscpho*gvdwc_scpho(j,i)+&
wpeppho*gvdwc_peppho(j,i)
+gradafm(j,i) &
+wliptran*gliptranc(j,i) &
+welec*gshieldc(j,i) &
- +welec*gshieldc_loc(j,) &
+ +welec*gshieldc_loc(j,i) &
+wcorr*gshieldc_ec(j,i) &
+wcorr*gshieldc_loc_ec(j,i) &
+wturn3*gshieldc_t3(j,i) &
rrij=1.0D0/(xj*xj+yj*yj+zj*zj)
rij=dsqrt(rrij)
sss=sscale(1.0d0/(rij*sigmaii(itypi,itypj)))
- sss_ele_cut=sscale_ele(1.0d0/(rij*sigma(itypi,itypj)))
- sss_ele_grad=sscagrad_ele(1.0d0/(rij*sigma(itypi,itypj)))
+ sss_ele_cut=sscale_ele(1.0d0/(rij))
+ sss_ele_grad=sscagrad_ele(1.0d0/(rij))
sss_grad=sscale_grad(1.0d0/(rij*sigmaii(itypi,itypj)))
if (sss_ele_cut.le.0.0) cycle
if (sss.lt.1.0d0) then
sigder=fac*sigder
fac=rij*fac
fac=fac+evdwij*(sss_ele_grad/sss_ele_cut&
- /sigma(itypi,itypj)*rij-sss_grad/(1.0-sss)*rij &
+ *rij-sss_grad/(1.0-sss)*rij &
/sigmaii(itypi,itypj))
! fac=0.0d0
! Calculate the radial part of the gradient
rij=dsqrt(rrij)
sss=sscale(1.0d0/(rij*sigmaii(itypi,itypj)))
sss_grad=sscale_grad(1.0d0/(rij*sigmaii(itypi,itypj)))
- sss_ele_cut=sscale_ele(1.0d0/(rij*sigma(itypi,itypj)))
- sss_ele_grad=sscagrad_ele(1.0d0/(rij*sigma(itypi,itypj)))
+ sss_ele_cut=sscale_ele(1.0d0/(rij))
+ sss_ele_grad=sscagrad_ele(1.0d0/(rij))
if (sss_ele_cut.le.0.0) cycle
if (sss.gt.0.0d0) then
sigder=fac*sigder
fac=rij*fac
fac=fac+evdwij*(sss_ele_grad/sss_ele_cut&
- /sigma(itypi,itypj)*rij+sss_grad/sss*rij &
+ *rij+sss_grad/sss*rij &
/sigmaii(itypi,itypj))
! fac=0.0d0
elseif(UNRES_MD_FF STREQUAL "E0LL2Y")
# set preprocesor flags
set(CPPFLAGS "PROCOR -DSPLITELE -DSCCORPDB" )
+elseif(UNRES_MD_FF STREQUAL "NEWCORR")
+ # set preprocesor flags
+ set(CPPFLAGS "PROCOR -DUNRES -DISNAN -DSPLITELE -DLANG0 -DNEWCORR -DCORRCD" )
elseif(UNRES_MD_FF STREQUAL "4P")
set(CPPFLAGS "SPLITELE -DLANG0 -DCRYST_BOND -DCRYST_THETA -DCRYST_SC -DSCCORPDB" )
endif(UNRES_MD_FF STREQUAL "GAB")
mnum=molnum(i)
i1=icont(1,i)
i2=icont(2,i)
- it1=itype(i1,molnum(i1))
- it2=itype(i2,molnum(i2))
-! print *,"CONTACT",i1,mnum,it1,it2
+ it1=itype(i1,1)
+ it2=itype(i2,1)
+ if (mnum.eq.0) mnum=1
+ print *,"CONTACT",i1,i2,mnum,it1,it2
write (iout,'(i3,2x,a,i4,2x,a,i4,5f8.3,3f10.5)') &
i,restyp(it1,mnum),i1,restyp(it2,mnum),i2,cscore(i),&
sc_cutoff(iabs(it1),iabs(it2)),ddsc(i),ddla(i),ddlb(i),&
i2=icont(2,i)
it1=itype(i1,1)
it2=itype(i2,1)
+ write(iout,*) "test",i1,i2,it1,it2
write (iout,'(i3,2x,a,i4,2x,a,i4)') &
i,restyp(it1,mnum),i1,restyp(it2,mnum),i2
enddo
!-----------------------------------------------------------------------------
use io_units
use wham_data
+ use control_data, only: tor_mode
!
use geometry_data, only:nres,boxxsize,boxysize,boxzsize
use energy_data
ww_all(16,iparm)=wvdwpp
ww_all(17,iparm)=wbond
ww_all(19,iparm)=wsccor
+ ww_all(42,iparm)=wcatprot
+ ww_all(41,iparm)=wcatcat
! Store bond parameters
vbldp0_all(iparm)=vbldp0
akp_all(iparm)=akp
sigc0_all(i,iparm)=sigc0(i)
enddo
#else
+ IF (tor_mode.eq.0) THEN
nthetyp_all(iparm)=nthetyp
ntheterm_all(iparm)=ntheterm
ntheterm2_all(iparm)=ntheterm2
enddo
enddo
enddo
+ ELSE
+ write(iout,*) "Need storing parameters"
+ ENDIF
#endif
#ifdef CRYST_SC
! Store the sidechain rotamer parameters
enddo
enddo
#endif
+ IF (tor_mode.eq.0) THEN
! Store the torsional parameters
do iblock=1,2
do i=-ntortyp+1,ntortyp-1
enddo
enddo
enddo
+ ELSE
+ write(iout,*) "NEED storing parameters"
+ ENDIF
! Store the parameters of electrostatic interactions
do i=1,2
do j=1,2
wvdwpp=ww_all(16,iparm)
wbond=ww_all(17,iparm)
wsccor=ww_all(19,iparm)
+ wcatprot=ww_all(42,iparm)
+ wcatcat=ww_all(41,iparm)
! Restore bond parameters
vbldp0=vbldp0_all(iparm)
akp=akp_all(iparm)
sigc0(i)=sigc0_all(i,iparm)
enddo
#else
+ IF (tor_mode.eq.0) THEN
nthetyp=nthetyp_all(iparm)
ntheterm=ntheterm_all(iparm)
ntheterm2=ntheterm2_all(iparm)
enddo
enddo
enddo
+ ELSE
+ write (iout,*) "Need storing parameters"
+ ENDIF
#endif
! Restore the sidechain rotamer parameters
#ifdef CRYST_SC
enddo
enddo
#endif
+ IF (tor_mode.eq.0) THEN
! Restore the torsional parameters
do iblock=1,2
do i=-ntortyp+1,ntortyp-1
enddo
enddo
enddo
+
! Restore parameters of the cumulants
do i=-nloctyp,nloctyp
do j=1,2
enddo
enddo
enddo
+ ELSE
+ write(iout,*) "need storing parameters"
+ ENDIF
! Restore the parameters of electrostatic interactions
do i=1,2
do j=1,2
use geometry_data
use energy_data
use control_data, only: maxterm,maxlor,maxterm_sccor,& !maxtor
- maxtermd_1,maxtermd_2 !,maxthetyp,maxthetyp1
+ maxtermd_1,maxtermd_2,tor_mode,scelemode !,maxthetyp,maxthetyp1
use MD_data
!el use MPI_data
!el use map_data
character(len=1) :: t1,t2,t3
character(len=1) :: onelett(4) = (/"G","A","P","D"/)
character(len=1) :: toronelet(-2:2) = (/"p","a","G","A","P"/)
- logical :: lprint
+ logical :: lprint,SPLIT_FOURIERTOR
real(kind=8),dimension(3,3,maxlob) :: blower !(3,3,maxlob)
character(len=800) :: controlcard
character(len=256) :: bondname_t,thetname_t,rotname_t,torname_t,&
!el integer ilen
!el external ilen
character(len=16) :: key
- integer :: iparm
+ integer :: iparm,nkcctyp
!el real(kind=8) :: ip,mp
real(kind=8) :: dwa16,akl,si,rri,epsij,rrij,sigeps,sigt1sq,epsijlip,&
sigt2sq,sigii1,sigii2,ratsig1,ratsig2,rsum_max,r_augm
real(kind=8) :: v0ij,v0ijsccor,v0ijsccor1,v0ijsccor2,v0ijsccor3,rjunk,&
res1
- integer :: i,j,ichir1,ichir2,k,l,m,kk,ii,mm,junk,lll,ll,llll,n
+ integer :: i,j,ichir1,ichir2,k,l,m,kk,ii,mm,junk,lll,ll,llll,n,jj
integer :: nlobi,iblock,maxinter,iscprol,ncatprotparm
+ character*3 string
+
!
! Body
!
wvdwpp=ww(16)
wbond=ww(18)
wsccor=ww(19)
- wcatcat=ww(44)
- wcatprot=ww(43)
+ wcatcat=ww(42)
+ wcatprot=ww(41)
endif
!
weights(17)=wbond
weights(18)=0 !scal14 !
weights(21)=wsccor
- weights(43)=wcatprot
- weights(44)=wcatcat
+ weights(42)=wcatprot
+ weights(41)=wcatcat
! el--------
call card_concat(controlcard,.false.)
! Read the parameters of Utheta determined from ab initio surfaces
! Kozlowska et al., J. Phys.: Condens. Matter 19 (2007) 285203
!
+ allocate(ithetyp(-ntyp1:ntyp1)) !(-ntyp1:ntyp1)
! write (iout,*) "tu dochodze"
+ IF (tor_mode.eq.0) THEN
+!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
read (ithep,*) nthetyp,ntheterm,ntheterm2,&
ntheterm3,nsingle,ndouble
nntheterm=max0(ntheterm,ntheterm2,ntheterm3)
!----------------------------------------------------
- allocate(ithetyp(-ntyp1:ntyp1)) !(-ntyp1:ntyp1)
+! allocate(ithetyp(-ntyp1:ntyp1)) !(-ntyp1:ntyp1)
allocate(aa0thet(-nthetyp-1:nthetyp+1,&
-nthetyp-1:nthetyp+1,-nthetyp-1:nthetyp+1,2))
!(-maxthetyp1:maxthetyp1,-maxthetyp1:maxthetyp1,-maxthetyp1:maxthetyp1,2)
!
! Control printout of the coefficients of virtual-bond-angle potentials
!
-do iblock=1,2
+ do iblock=1,2
if (lprint) then
write (iout,'(//a)') 'Parameter of virtual-bond-angle potential'
do i=1,nthetyp+1
enddo
call flush(iout)
endif
-enddo
+ enddo
+ ELSE
+!C here will be the apropriate recalibrating for D-aminoacid
+ read (ithep,*) nthetyp
+ allocate(nbend_kcc_Tb(-nthetyp:nthetyp))
+ allocate(v1bend_chyb(0:36,-nthetyp:nthetyp))
+ do i=-nthetyp+1,nthetyp-1
+ read (ithep,*) nbend_kcc_Tb(i)
+ do j=0,nbend_kcc_Tb(i)
+ read (ithep,*) ijunk,v1bend_chyb(j,i)
+ enddo
+ enddo
+ if (lprint) then
+ write (iout,'(a)') &
+ "Parameters of the valence-only potentials"
+ do i=-nthetyp+1,nthetyp-1
+ write (iout,'(2a)') "Type ",toronelet(i)
+ do k=0,nbend_kcc_Tb(i)
+ write(iout,'(i5,f15.5)') k,v1bend_chyb(k,i)
+ enddo
+ enddo
+ endif
+ ENDIF ! TOR_MODE
+
#endif
!-------------------------------------------
allocate(nlob(ntyp1)) !(ntyp1)
enddo
#endif
close(irotam)
+
+ read (ifourier,*) nloctyp
+!el write(iout,*)"nloctyp",nloctyp
+ SPLIT_FOURIERTOR = nloctyp.lt.0
+ nloctyp = iabs(nloctyp)
+#ifdef NEWCORR
+ if (.not.allocated(itype2loc)) allocate(itype2loc(-ntyp1:ntyp1))
+ print *,"shape",shape(itype2loc)
+ allocate(iloctyp(-nloctyp:nloctyp))
+ allocate(bnew1(3,2,-nloctyp:nloctyp))
+ allocate(bnew2(3,2,-nloctyp:nloctyp))
+ allocate(ccnew(3,2,-nloctyp:nloctyp))
+ allocate(ddnew(3,2,-nloctyp:nloctyp))
+ allocate(e0new(3,-nloctyp:nloctyp))
+ allocate(eenew(2,2,2,-nloctyp:nloctyp))
+ allocate(bnew1tor(3,2,-nloctyp:nloctyp))
+ allocate(bnew2tor(3,2,-nloctyp:nloctyp))
+ allocate(ccnewtor(3,2,-nloctyp:nloctyp))
+ allocate(ddnewtor(3,2,-nloctyp:nloctyp))
+ allocate(e0newtor(3,-nloctyp:nloctyp))
+ allocate(eenewtor(2,2,2,-nloctyp:nloctyp))
+
+ read (ifourier,*) (itype2loc(i),i=1,ntyp)
+ read (ifourier,*) (iloctyp(i),i=0,nloctyp-1)
+ itype2loc(ntyp1)=nloctyp
+ iloctyp(nloctyp)=ntyp1
+ do i=1,ntyp1
+ itype2loc(-i)=-itype2loc(i)
+ enddo
+#else
+ allocate(iloctyp(-nloctyp:nloctyp))
+ allocate(itype2loc(-ntyp1:ntyp1))
+ iloctyp(0)=10
+ iloctyp(1)=9
+ iloctyp(2)=20
+ iloctyp(3)=ntyp1
+#endif
+ do i=1,nloctyp
+ iloctyp(-i)=-iloctyp(i)
+ enddo
+!c write (iout,*) "itype2loc",(itype2loc(i),i=1,ntyp1)
+!c write (iout,*) "nloctyp",nloctyp,
+!c & " iloctyp",(iloctyp(i),i=0,nloctyp)
+!c write (iout,*) "itype2loc",(itype2loc(i),i=1,ntyp1)
+!c write (iout,*) "nloctyp",nloctyp,
+!c & " iloctyp",(iloctyp(i),i=0,nloctyp)
+#ifdef NEWCORR
+ do i=0,nloctyp-1
+!c write (iout,*) "NEWCORR",i
+ read (ifourier,*)
+ do ii=1,3
+ do j=1,2
+ read (ifourier,*) bnew1(ii,j,i)
+ enddo
+ enddo
+!c write (iout,*) "NEWCORR BNEW1"
+!c write (iout,*) ((bnew1(ii,j,i),ii=1,3),j=1,2)
+ do ii=1,3
+ do j=1,2
+ read (ifourier,*) bnew2(ii,j,i)
+ enddo
+ enddo
+!c write (iout,*) "NEWCORR BNEW2"
+!c write (iout,*) ((bnew2(ii,j,i),ii=1,3),j=1,2)
+ do kk=1,3
+ read (ifourier,*) ccnew(kk,1,i)
+ read (ifourier,*) ccnew(kk,2,i)
+ enddo
+!c write (iout,*) "NEWCORR CCNEW"
+!c write (iout,*) ((ccnew(ii,j,i),ii=1,3),j=1,2)
+ do kk=1,3
+ read (ifourier,*) ddnew(kk,1,i)
+ read (ifourier,*) ddnew(kk,2,i)
+ enddo
+!c write (iout,*) "NEWCORR DDNEW"
+!c write (iout,*) ((ddnew(ii,j,i),ii=1,3),j=1,2)
+ do ii=1,2
+ do jj=1,2
+ do kk=1,2
+ read (ifourier,*) eenew(ii,jj,kk,i)
+ enddo
+ enddo
+ enddo
+!c write (iout,*) "NEWCORR EENEW1"
+!c write(iout,*)(((eenew(ii,jj,kk,i),kk=1,2),jj=1,2),ii=1,2)
+ do ii=1,3
+ read (ifourier,*) e0new(ii,i)
+ enddo
+!c write (iout,*) (e0new(ii,i),ii=1,3)
+ enddo
+!c write (iout,*) "NEWCORR EENEW"
+ do i=0,nloctyp-1
+ do ii=1,3
+ ccnew(ii,1,i)=ccnew(ii,1,i)/2
+ ccnew(ii,2,i)=ccnew(ii,2,i)/2
+ ddnew(ii,1,i)=ddnew(ii,1,i)/2
+ ddnew(ii,2,i)=ddnew(ii,2,i)/2
+ enddo
+ enddo
+ do i=1,nloctyp-1
+ do ii=1,3
+ bnew1(ii,1,-i)= bnew1(ii,1,i)
+ bnew1(ii,2,-i)=-bnew1(ii,2,i)
+ bnew2(ii,1,-i)= bnew2(ii,1,i)
+ bnew2(ii,2,-i)=-bnew2(ii,2,i)
+ enddo
+ do ii=1,3
+!c ccnew(ii,1,i)=ccnew(ii,1,i)/2
+!c ccnew(ii,2,i)=ccnew(ii,2,i)/2
+!c ddnew(ii,1,i)=ddnew(ii,1,i)/2
+!c ddnew(ii,2,i)=ddnew(ii,2,i)/2
+ ccnew(ii,1,-i)=ccnew(ii,1,i)
+ ccnew(ii,2,-i)=-ccnew(ii,2,i)
+ ddnew(ii,1,-i)=ddnew(ii,1,i)
+ ddnew(ii,2,-i)=-ddnew(ii,2,i)
+ enddo
+ e0new(1,-i)= e0new(1,i)
+ e0new(2,-i)=-e0new(2,i)
+ e0new(3,-i)=-e0new(3,i)
+ do kk=1,2
+ eenew(kk,1,1,-i)= eenew(kk,1,1,i)
+ eenew(kk,1,2,-i)=-eenew(kk,1,2,i)
+ eenew(kk,2,1,-i)=-eenew(kk,2,1,i)
+ eenew(kk,2,2,-i)= eenew(kk,2,2,i)
+ enddo
+ enddo
+ if (lprint) then
+ write (iout,'(a)') "Coefficients of the multibody terms"
+ do i=-nloctyp+1,nloctyp-1
+ write (iout,*) "Type: ",onelet(iloctyp(i))
+ write (iout,*) "Coefficients of the expansion of B1"
+ do j=1,2
+ write (iout,'(3hB1(,i1,1h),3f10.5)') j,(bnew1(k,j,i),k=1,3)
+ enddo
+ write (iout,*) "Coefficients of the expansion of B2"
+ do j=1,2
+ write (iout,'(3hB2(,i1,1h),3f10.5)') j,(bnew2(k,j,i),k=1,3)
+ enddo
+ write (iout,*) "Coefficients of the expansion of C"
+ write (iout,'(3hC11,3f10.5)') (ccnew(j,1,i),j=1,3)
+ write (iout,'(3hC12,3f10.5)') (ccnew(j,2,i),j=1,3)
+ write (iout,*) "Coefficients of the expansion of D"
+ write (iout,'(3hD11,3f10.5)') (ddnew(j,1,i),j=1,3)
+ write (iout,'(3hD12,3f10.5)') (ddnew(j,2,i),j=1,3)
+ write (iout,*) "Coefficients of the expansion of E"
+ write (iout,'(2hE0,3f10.5)') (e0new(j,i),j=1,3)
+ do j=1,2
+ do k=1,2
+ write (iout,'(1hE,2i1,2f10.5)') j,k,(eenew(l,j,k,i),l=1,2)
+ enddo
+ enddo
+ enddo
+ endif
+ IF (SPLIT_FOURIERTOR) THEN
+ do i=0,nloctyp-1
+!c write (iout,*) "NEWCORR TOR",i
+ read (ifourier,*)
+ do ii=1,3
+ do j=1,2
+ read (ifourier,*) bnew1tor(ii,j,i)
+ enddo
+ enddo
+!c write (iout,*) "NEWCORR BNEW1 TOR"
+!c write (iout,*) ((bnew1tor(ii,j,i),ii=1,3),j=1,2)
+ do ii=1,3
+ do j=1,2
+ read (ifourier,*) bnew2tor(ii,j,i)
+ enddo
+ enddo
+!c write (iout,*) "NEWCORR BNEW2 TOR"
+!c write (iout,*) ((bnew2tor(ii,j,i),ii=1,3),j=1,2)
+ do kk=1,3
+ read (ifourier,*) ccnewtor(kk,1,i)
+ read (ifourier,*) ccnewtor(kk,2,i)
+ enddo
+!c write (iout,*) "NEWCORR CCNEW TOR"
+!c write (iout,*) ((ccnew(ii,j,i),ii=1,3),j=1,2)
+ do kk=1,3
+ read (ifourier,*) ddnewtor(kk,1,i)
+ read (ifourier,*) ddnewtor(kk,2,i)
+ enddo
+!c write (iout,*) "NEWCORR DDNEW TOR"
+!c write (iout,*) ((ddnewtor(ii,j,i),ii=1,3),j=1,2)
+ do ii=1,2
+ do jj=1,2
+ do kk=1,2
+ read (ifourier,*) eenewtor(ii,jj,kk,i)
+ enddo
+ enddo
+ enddo
+!c write (iout,*) "NEWCORR EENEW1 TOR"
+!c write(iout,*)(((eenewtor(ii,jj,kk,i),kk=1,2),jj=1,2),ii=1,2)
+ do ii=1,3
+ read (ifourier,*) e0newtor(ii,i)
+ enddo
+!c write (iout,*) (e0newtor(ii,i),ii=1,3)
+ enddo
+!c write (iout,*) "NEWCORR EENEW TOR"
+ do i=0,nloctyp-1
+ do ii=1,3
+ ccnewtor(ii,1,i)=ccnewtor(ii,1,i)/2
+ ccnewtor(ii,2,i)=ccnewtor(ii,2,i)/2
+ ddnewtor(ii,1,i)=ddnewtor(ii,1,i)/2
+ ddnewtor(ii,2,i)=ddnewtor(ii,2,i)/2
+ enddo
+ enddo
+ do i=1,nloctyp-1
+ do ii=1,3
+ bnew1tor(ii,1,-i)= bnew1tor(ii,1,i)
+ bnew1tor(ii,2,-i)=-bnew1tor(ii,2,i)
+ bnew2tor(ii,1,-i)= bnew2tor(ii,1,i)
+ bnew2tor(ii,2,-i)=-bnew2tor(ii,2,i)
+ enddo
+ do ii=1,3
+ ccnewtor(ii,1,-i)=ccnewtor(ii,1,i)
+ ccnewtor(ii,2,-i)=-ccnewtor(ii,2,i)
+ ddnewtor(ii,1,-i)=ddnewtor(ii,1,i)
+ ddnewtor(ii,2,-i)=-ddnewtor(ii,2,i)
+ enddo
+ e0newtor(1,-i)= e0newtor(1,i)
+ e0newtor(2,-i)=-e0newtor(2,i)
+ e0newtor(3,-i)=-e0newtor(3,i)
+ do kk=1,2
+ eenewtor(kk,1,1,-i)= eenewtor(kk,1,1,i)
+ eenewtor(kk,1,2,-i)=-eenewtor(kk,1,2,i)
+ eenewtor(kk,2,1,-i)=-eenewtor(kk,2,1,i)
+ eenewtor(kk,2,2,-i)= eenewtor(kk,2,2,i)
+ enddo
+ enddo
+ if (lprint) then
+ write (iout,'(a)') &
+ "Single-body coefficients of the torsional potentials"
+ do i=-nloctyp+1,nloctyp-1
+ write (iout,*) "Type: ",onelet(iloctyp(i))
+ write (iout,*) "Coefficients of the expansion of B1tor"
+ do j=1,2
+ write (iout,'(3hB1(,i1,1h),3f10.5)') &
+ j,(bnew1tor(k,j,i),k=1,3)
+ enddo
+ write (iout,*) "Coefficients of the expansion of B2tor"
+ do j=1,2
+ write (iout,'(3hB2(,i1,1h),3f10.5)') &
+ j,(bnew2tor(k,j,i),k=1,3)
+ enddo
+ write (iout,*) "Coefficients of the expansion of Ctor"
+ write (iout,'(3hC11,3f10.5)') (ccnewtor(j,1,i),j=1,3)
+ write (iout,'(3hC12,3f10.5)') (ccnewtor(j,2,i),j=1,3)
+ write (iout,*) "Coefficients of the expansion of Dtor"
+ write (iout,'(3hD11,3f10.5)') (ddnewtor(j,1,i),j=1,3)
+ write (iout,'(3hD12,3f10.5)') (ddnewtor(j,2,i),j=1,3)
+ write (iout,*) "Coefficients of the expansion of Etor"
+ write (iout,'(2hE0,3f10.5)') (e0newtor(j,i),j=1,3)
+ do j=1,2
+ do k=1,2
+ write (iout,'(1hE,2i1,2f10.5)') &
+ j,k,(eenewtor(l,j,k,i),l=1,2)
+ enddo
+ enddo
+ enddo
+ endif
+ ELSE
+ do i=-nloctyp+1,nloctyp-1
+ do ii=1,3
+ do j=1,2
+ bnew1tor(ii,j,i)=bnew1(ii,j,i)
+ enddo
+ enddo
+ do ii=1,3
+ do j=1,2
+ bnew2tor(ii,j,i)=bnew2(ii,j,i)
+ enddo
+ enddo
+ do ii=1,3
+ ccnewtor(ii,1,i)=ccnew(ii,1,i)
+ ccnewtor(ii,2,i)=ccnew(ii,2,i)
+ ddnewtor(ii,1,i)=ddnew(ii,1,i)
+ ddnewtor(ii,2,i)=ddnew(ii,2,i)
+ enddo
+ enddo
+ ENDIF !SPLIT_FOURIER_TOR
+#else
+ allocate(ccold(2,2,-nloctyp-1:nloctyp+1))
+ allocate(ddold(2,2,-nloctyp-1:nloctyp+1))
+ allocate(eeold(2,2,-nloctyp-1:nloctyp+1))
+ allocate(b(13,-nloctyp-1:nloctyp+1))
+ if (lprint) &
+ write (iout,*) "Coefficients of the expansion of Eloc(l1,l2)"
+ do i=0,nloctyp-1
+ read (ifourier,*)
+ read (ifourier,*) (b(ii,i),ii=1,13)
+ if (lprint) then
+ write (iout,*) 'Type ',onelet(iloctyp(i))
+ write (iout,'(a,i2,a,f10.5)') ('b(',ii,')=',b(ii,i),ii=1,13)
+ endif
+ if (i.gt.0) then
+ b(2,-i)= b(2,i)
+ b(3,-i)= b(3,i)
+ b(4,-i)=-b(4,i)
+ b(5,-i)=-b(5,i)
+ endif
+ CCold(1,1,i)= b(7,i)
+ CCold(2,2,i)=-b(7,i)
+ CCold(2,1,i)= b(9,i)
+ CCold(1,2,i)= b(9,i)
+ CCold(1,1,-i)= b(7,i)
+ CCold(2,2,-i)=-b(7,i)
+ CCold(2,1,-i)=-b(9,i)
+ CCold(1,2,-i)=-b(9,i)
+ DDold(1,1,i)= b(6,i)
+ DDold(2,2,i)=-b(6,i)
+ DDold(2,1,i)= b(8,i)
+ DDold(1,2,i)= b(8,i)
+ DDold(1,1,-i)= b(6,i)
+ DDold(2,2,-i)=-b(6,i)
+ DDold(2,1,-i)=-b(8,i)
+ DDold(1,2,-i)=-b(8,i)
+ EEold(1,1,i)= b(10,i)+b(11,i)
+ EEold(2,2,i)=-b(10,i)+b(11,i)
+ EEold(2,1,i)= b(12,i)-b(13,i)
+ EEold(1,2,i)= b(12,i)+b(13,i)
+ EEold(1,1,-i)= b(10,i)+b(11,i)
+ EEold(2,2,-i)=-b(10,i)+b(11,i)
+ EEold(2,1,-i)=-b(12,i)+b(13,i)
+ EEold(1,2,-i)=-b(12,i)-b(13,i)
+ write(iout,*) "TU DOCHODZE"
+ print *,"JESTEM"
+ enddo
+ if (lprint) then
+ write (iout,*)
+ write (iout,*) &
+ "Coefficients of the cumulants (independent of valence angles)"
+ do i=-nloctyp+1,nloctyp-1
+ write (iout,*) 'Type ',onelet(iloctyp(i))
+ write (iout,*) 'B1'
+ write(iout,'(2f10.5)') B(3,i),B(5,i)
+ write (iout,*) 'B2'
+ write(iout,'(2f10.5)') B(2,i),B(4,i)
+ write (iout,*) 'CC'
+ do j=1,2
+ write (iout,'(2f10.5)') CCold(j,1,i),CCold(j,2,i)
+ enddo
+ write(iout,*) 'DD'
+ do j=1,2
+ write (iout,'(2f10.5)') DDold(j,1,i),DDold(j,2,i)
+ enddo
+ write(iout,*) 'EE'
+ do j=1,2
+ write (iout,'(2f10.5)') EEold(j,1,i),EEold(j,2,i)
+ enddo
+ enddo
+ endif
+#endif
#ifdef CRYST_TOR
!
! Read torsional parameters in old format
!
! Read torsional parameters
!
+ IF (TOR_MODE.eq.0) THEN
+
allocate(itortyp(-ntyp1:ntyp1)) !(-ntyp1:ntyp1)
read (itorp,*) ntortyp
enddo
enddo
endif
+ ELSE IF (TOR_MODE.eq.1) THEN
+
+!C read valence-torsional parameters
+ read (itorp,*) ntortyp
+ nkcctyp=ntortyp
+ write (iout,*) "Valence-torsional parameters read in ntortyp",&
+ ntortyp
+ read (itorp,*) (itortyp(i),i=1,ntyp)
+ write (iout,*) "itortyp_kcc",(itortyp(i),i=1,ntyp)
+#ifndef NEWCORR
+ do i=1,ntyp1
+ itype2loc(i)=itortyp(i)
+ enddo
+#endif
+ do i=-ntyp,-1
+ itortyp(i)=-itortyp(-i)
+ enddo
+ do i=-ntortyp+1,ntortyp-1
+ do j=-ntortyp+1,ntortyp-1
+!C first we read the cos and sin gamma parameters
+ read (itorp,'(13x,a)') string
+ write (iout,*) i,j,string
+ read (itorp,*) &
+ nterm_kcc(j,i),nterm_kcc_Tb(j,i)
+!C read (itorkcc,*,end=121,err=121) nterm_kcc_Tb(j,i)
+ do k=1,nterm_kcc(j,i)
+ do l=1,nterm_kcc_Tb(j,i)
+ do ll=1,nterm_kcc_Tb(j,i)
+ read (itorp,*) ii,jj,kk, &
+ v1_kcc(ll,l,k,j,i),v2_kcc(ll,l,k,j,i)
+ enddo
+ enddo
+ enddo
+ enddo
+ enddo
+ ELSE
+#ifdef NEWCORR
+!c AL 4/8/16: Calculate coefficients from one-body parameters
+ ntortyp=nloctyp
+ allocate(itortyp(-ntyp1:ntyp1)) !(-ntyp1:ntyp1)
+ allocate(nterm_kcc(-ntyp1:ntyp1,-ntyp1:ntyp1))
+ allocate(nterm_kcc_Tb(-ntyp1:ntyp1,-ntyp1:ntyp1))
+ allocate(v1_kcc(6,6,6,-ntyp1:ntyp1,-ntyp1:ntyp1))
+ allocate(v2_kcc(6,6,6,-ntyp1:ntyp1,-ntyp1:ntyp1))
+
+ do i=-ntyp1,ntyp1
+ print *,i,itortyp(i)
+ itortyp(i)=itype2loc(i)
+ enddo
+ write (iout,*) &
+ "Val-tor parameters calculated from cumulant coefficients ntortyp"&
+ ,ntortyp
+ do i=-ntortyp+1,ntortyp-1
+ do j=-ntortyp+1,ntortyp-1
+ nterm_kcc(j,i)=2
+ nterm_kcc_Tb(j,i)=3
+ do k=1,nterm_kcc_Tb(j,i)
+ do l=1,nterm_kcc_Tb(j,i)
+ v1_kcc(k,l,1,i,j)=bnew1tor(k,1,i)*bnew2tor(l,1,j)&
+ +bnew1tor(k,2,i)*bnew2tor(l,2,j)
+ v2_kcc(k,l,1,i,j)=bnew1tor(k,1,i)*bnew2tor(l,2,j)&
+ +bnew1tor(k,2,i)*bnew2tor(l,1,j)
+ enddo
+ enddo
+ do k=1,nterm_kcc_Tb(j,i)
+ do l=1,nterm_kcc_Tb(j,i)
+#ifdef CORRCD
+ v1_kcc(k,l,2,i,j)=-(ccnewtor(k,1,i)*ddnewtor(l,1,j) &
+ -ccnewtor(k,2,i)*ddnewtor(l,2,j))
+ v2_kcc(k,l,2,i,j)=-(ccnewtor(k,2,i)*ddnewtor(l,1,j) &
+ +ccnewtor(k,1,i)*ddnewtor(l,2,j))
+#else
+ v1_kcc(k,l,2,i,j)=-0.25*(ccnewtor(k,1,i)*ddnewtor(l,1,j) &
+ -ccnewtor(k,2,i)*ddnewtor(l,2,j))
+ v2_kcc(k,l,2,i,j)=-0.25*(ccnewtor(k,2,i)*ddnewtor(l,1,j) &
+ +ccnewtor(k,1,i)*ddnewtor(l,2,j))
+#endif
+ enddo
+ enddo
+!c f(theta,gamma)=-(b21(theta)*b11(theta)+b12(theta)*b22(theta))*cos(gamma)-(b22(theta)*b11(theta)+b21(theta)*b12(theta))*sin(gamma)+(c11(theta)*d11(theta)-c12(theta)*d12(theta))*cos(2*gamma)+(c12(theta)*d11(theta)+c11(theta)*d12(theta))*sin(2*gamma)
+ enddo
+ enddo
+#else
+ write (iout,*) "TOR_MODE>1 only with NEWCORR"
+ stop
+#endif
+ ENDIF ! TOR_MODE
+ if (tor_mode.gt.0 .and. lprint) then
+!c Print valence-torsional parameters
+ write (iout,'(a)') &
+ "Parameters of the valence-torsional potentials"
+ do i=-ntortyp+1,ntortyp-1
+ do j=-ntortyp+1,ntortyp-1
+ write (iout,'(3a)') "Type ",toronelet(i),toronelet(j)
+ write (iout,'(3a5,2a15)') "itor","ival","jval","v_kcc","v2_kcc"
+ do k=1,nterm_kcc(j,i)
+ do l=1,nterm_kcc_Tb(j,i)
+ do ll=1,nterm_kcc_Tb(j,i)
+ write (iout,'(3i5,2f15.4)')&
+ k,l-1,ll-1,v1_kcc(ll,l,k,j,i),v2_kcc(ll,l,k,j,i)
+ enddo
+ enddo
+ enddo
+ enddo
+ enddo
+ endif
+
#endif
!elwrite(iout,*) "parmread kontrol sc-bb"
! Read of Side-chain backbone correlation parameters
enddo
enddo
endif
-!
-! 9/18/99 (AL) Read coefficients of the Fourier expansion of the local
-! interaction energy of the Gly, Ala, and Pro prototypes.
-!
- read (ifourier,*) nloctyp
-!el write(iout,*)"nloctyp",nloctyp
-!el from module energy-------
- allocate(b1(2,-nloctyp-1:nloctyp+1)) !(2,-maxtor:maxtor)
- allocate(b2(2,-nloctyp-1:nloctyp+1)) !(2,-maxtor:maxtor)
- allocate(b1tilde(2,-nloctyp-1:nloctyp+1)) !(2,-maxtor:maxtor)
- allocate(cc(2,2,-nloctyp-1:nloctyp+1))
- allocate(dd(2,2,-nloctyp-1:nloctyp+1))
- allocate(ee(2,2,-nloctyp-1:nloctyp+1))
- allocate(ctilde(2,2,-nloctyp-1:nloctyp+1))
- allocate(dtilde(2,2,-nloctyp-1:nloctyp+1)) !(2,2,-maxtor:maxtor)
- do i=1,2
- do ii=-nloctyp-1,nloctyp+1
- b1(i,ii)=0.0d0
- b2(i,ii)=0.0d0
- b1tilde(i,ii)=0.0d0
- do j=1,2
- cc(j,i,ii)=0.0d0
- dd(j,i,ii)=0.0d0
- ee(j,i,ii)=0.0d0
- ctilde(j,i,ii)=0.0d0
- dtilde(j,i,ii)=0.0d0
- enddo
- enddo
- enddo
-!--------------------------------
- allocate(b(13,0:nloctyp))
-
- do i=0,nloctyp-1
- read (ifourier,*)
- read (ifourier,*) (b(ii,i),ii=1,13)
- if (lprint) then
- write (iout,*) 'Type',i
- write (iout,'(a,i2,a,f10.5)') ('b(',ii,')=',b(ii,i),ii=1,13)
- endif
- B1(1,i) = b(3,i)
- B1(2,i) = b(5,i)
- B1(1,-i) = b(3,i)
- B1(2,-i) = -b(5,i)
-! b1(1,i)=0.0d0
-! b1(2,i)=0.0d0
- B1tilde(1,i) = b(3,i)
- B1tilde(2,i) =-b(5,i)
- B1tilde(1,-i) =-b(3,i)
- B1tilde(2,-i) =b(5,i)
-! b1tilde(1,i)=0.0d0
-! b1tilde(2,i)=0.0d0
- B2(1,i) = b(2,i)
- B2(2,i) = b(4,i)
- B2(1,-i) =b(2,i)
- B2(2,-i) =-b(4,i)
-
-! b2(1,i)=0.0d0
-! b2(2,i)=0.0d0
- CC(1,1,i)= b(7,i)
- CC(2,2,i)=-b(7,i)
- CC(2,1,i)= b(9,i)
- CC(1,2,i)= b(9,i)
- CC(1,1,-i)= b(7,i)
- CC(2,2,-i)=-b(7,i)
- CC(2,1,-i)=-b(9,i)
- CC(1,2,-i)=-b(9,i)
-! CC(1,1,i)=0.0d0
-! CC(2,2,i)=0.0d0
-! CC(2,1,i)=0.0d0
-! CC(1,2,i)=0.0d0
- Ctilde(1,1,i)=b(7,i)
- Ctilde(1,2,i)=b(9,i)
- Ctilde(2,1,i)=-b(9,i)
- Ctilde(2,2,i)=b(7,i)
- Ctilde(1,1,-i)=b(7,i)
- Ctilde(1,2,-i)=-b(9,i)
- Ctilde(2,1,-i)=b(9,i)
- Ctilde(2,2,-i)=b(7,i)
-
-! Ctilde(1,1,i)=0.0d0
-! Ctilde(1,2,i)=0.0d0
-! Ctilde(2,1,i)=0.0d0
-! Ctilde(2,2,i)=0.0d0
- DD(1,1,i)= b(6,i)
- DD(2,2,i)=-b(6,i)
- DD(2,1,i)= b(8,i)
- DD(1,2,i)= b(8,i)
- DD(1,1,-i)= b(6,i)
- DD(2,2,-i)=-b(6,i)
- DD(2,1,-i)=-b(8,i)
- DD(1,2,-i)=-b(8,i)
-! DD(1,1,i)=0.0d0
-! DD(2,2,i)=0.0d0
-! DD(2,1,i)=0.0d0
-! DD(1,2,i)=0.0d0
- Dtilde(1,1,i)=b(6,i)
- Dtilde(1,2,i)=b(8,i)
- Dtilde(2,1,i)=-b(8,i)
- Dtilde(2,2,i)=b(6,i)
- Dtilde(1,1,-i)=b(6,i)
- Dtilde(1,2,-i)=-b(8,i)
- Dtilde(2,1,-i)=b(8,i)
- Dtilde(2,2,-i)=b(6,i)
-
-! Dtilde(1,1,i)=0.0d0
-! Dtilde(1,2,i)=0.0d0
-! Dtilde(2,1,i)=0.0d0
-! Dtilde(2,2,i)=0.0d0
- EE(1,1,i)= b(10,i)+b(11,i)
- EE(2,2,i)=-b(10,i)+b(11,i)
- EE(2,1,i)= b(12,i)-b(13,i)
- EE(1,2,i)= b(12,i)+b(13,i)
- EE(1,1,-i)= b(10,i)+b(11,i)
- EE(2,2,-i)=-b(10,i)+b(11,i)
- EE(2,1,-i)=-b(12,i)+b(13,i)
- EE(1,2,-i)=-b(12,i)-b(13,i)
-
-! ee(1,1,i)=1.0d0
-! ee(2,2,i)=1.0d0
-! ee(2,1,i)=0.0d0
-! ee(1,2,i)=0.0d0
-! ee(2,1,i)=ee(1,2,i)
- enddo
- if (lprint) then
- do i=1,nloctyp
- write (iout,*) 'Type',i
- write (iout,*) 'B1'
-! write (iout,'(f10.5)') B1(:,i)
- write(iout,*) B1(1,i),B1(2,i)
- write (iout,*) 'B2'
-! write (iout,'(f10.5)') B2(:,i)
- write(iout,*) B2(1,i),B2(2,i)
- write (iout,*) 'CC'
- do j=1,2
- write (iout,'(2f10.5)') CC(j,1,i),CC(j,2,i)
- enddo
- write(iout,*) 'DD'
- do j=1,2
- write (iout,'(2f10.5)') DD(j,1,i),DD(j,2,i)
- enddo
- write(iout,*) 'EE'
- do j=1,2
- write (iout,'(2f10.5)') EE(j,1,i),EE(j,2,i)
- enddo
- enddo
- endif
!
! Read electrostatic-interaction parameters
!
!---------------------- GB or BP potential -----------------------------
case (3:4)
! 30 do i=1,ntyp
+ if (scelemode.eq.0) then
do i=1,ntyp
read (isidep,*)(eps(i,j),j=i,ntyp)
enddo
write (iout,'(a3,6x,4f10.5)') (restyp(i,molnum(i)),sigma0(i),sigii(i),&
chip(i),alp(i),i=1,ntyp)
endif
+ else
+ allocate(icharge(ntyp1))
+! print *,ntyp,icharge(i)
+ icharge(:)=0
+ read (isidep,*) (icharge(i),i=1,ntyp)
+ print *,ntyp,icharge(i)
+! if(.not.allocated(eps)) allocate(eps(-ntyp
+ write (2,*) "icharge",(icharge(i),i=1,ntyp)
+ allocate(alphapol(ntyp,ntyp),epshead(ntyp,ntyp),sig0head(ntyp,ntyp))
+ allocate(sigiso1(ntyp,ntyp),rborn(ntyp,ntyp),sigmap1(ntyp,ntyp))
+ allocate(sigmap2(ntyp,ntyp),sigiso2(ntyp,ntyp))
+ allocate(chis(ntyp,ntyp),wquad(ntyp,ntyp),chipp(ntyp,ntyp))
+ allocate(epsintab(ntyp,ntyp))
+ allocate(dtail(2,ntyp,ntyp))
+ print *,"control line 1"
+ allocate(alphasur(4,ntyp,ntyp),alphiso(4,ntyp,ntyp))
+ allocate(wqdip(2,ntyp,ntyp))
+ allocate(wstate(4,ntyp,ntyp))
+ allocate(dhead(2,2,ntyp,ntyp))
+ allocate(nstate(ntyp,ntyp))
+ allocate(debaykap(ntyp,ntyp))
+ print *,"control line 2"
+ if (.not.allocated(sigma)) allocate(sigma(0:ntyp1,0:ntyp1))
+ if (.not.allocated(chi)) allocate(chi(ntyp1,ntyp1)) !(ntyp,ntyp)
+
+ do i=1,ntyp
+ do j=1,i
+! write (*,*) "Im in ALAB", i, " ", j
+ read(isidep,*) &
+ eps(i,j),sigma(i,j),chi(i,j),chi(j,i),chipp(i,j),chipp(j,i), &
+ (alphasur(k,i,j),k=1,4),sigmap1(i,j),sigmap2(i,j), &
+ chis(i,j),chis(j,i), &
+ nstate(i,j),(wstate(k,i,j),k=1,4), &
+ dhead(1,1,i,j),dhead(1,2,i,j),dhead(2,1,i,j),dhead(2,2,i,j),&
+ dtail(1,i,j),dtail(2,i,j), &
+ epshead(i,j),sig0head(i,j), &
+ rborn(i,j),rborn(j,i),(wqdip(k,i,j),k=1,2),wquad(i,j), &
+ alphapol(i,j),alphapol(j,i), &
+ (alphiso(k,i,j),k=1,4),sigiso1(i,j),sigiso2(i,j),epsintab(i,j),debaykap(i,j)
+! print *,eps(i,j),sigma(i,j),"SIGMAP",i,j,sigmap1(i,j),sigmap2(j,i)
+ END DO
+ END DO
+ DO i = 1, ntyp
+ DO j = i+1, ntyp
+ eps(i,j) = eps(j,i)
+ sigma(i,j) = sigma(j,i)
+ sigmap1(i,j)=sigmap1(j,i)
+ sigmap2(i,j)=sigmap2(j,i)
+ sigiso1(i,j)=sigiso1(j,i)
+ sigiso2(i,j)=sigiso2(j,i)
+! print *,"ATU",sigma(j,i),sigma(i,j),i,j
+ nstate(i,j) = nstate(j,i)
+ dtail(1,i,j) = dtail(1,j,i)
+ dtail(2,i,j) = dtail(2,j,i)
+ DO k = 1, 4
+ alphasur(k,i,j) = alphasur(k,j,i)
+ wstate(k,i,j) = wstate(k,j,i)
+ alphiso(k,i,j) = alphiso(k,j,i)
+ END DO
+
+ dhead(2,1,i,j) = dhead(1,1,j,i)
+ dhead(2,2,i,j) = dhead(1,2,j,i)
+ dhead(1,1,i,j) = dhead(2,1,j,i)
+ dhead(1,2,i,j) = dhead(2,2,j,i)
+
+ epshead(i,j) = epshead(j,i)
+ sig0head(i,j) = sig0head(j,i)
+
+ DO k = 1, 2
+ wqdip(k,i,j) = wqdip(k,j,i)
+ END DO
+
+ wquad(i,j) = wquad(j,i)
+ epsintab(i,j) = epsintab(j,i)
+ debaykap(i,j)=debaykap(j,i)
+! if (epsintab(i,j).ne.1.0) print *,"WHAT?",i,j,epsintab(i,j)
+ END DO
+ END DO
+ endif
+
! goto 50
!--------------------- GBV potential -----------------------------------
case (5)
!el from module energy - COMMON.INTERACT-------
! allocate(aa(ntyp1,ntyp1),bb(ntyp1,ntyp1),chi(ntyp1,ntyp1)) !(ntyp,ntyp)
- allocate(aa_aq(ntyp1,ntyp1),bb_aq(ntyp1,ntyp1),chi(ntyp1,ntyp1)) !(ntyp,ntyp)
+ if (.not.allocated(chi)) allocate(chi(ntyp1,ntyp1))
+ allocate(aa_aq(ntyp1,ntyp1),bb_aq(ntyp1,ntyp1)) !(ntyp,ntyp)
allocate(aa_lip(ntyp1,ntyp1),bb_lip(ntyp1,ntyp1)) !(ntyp,ntyp)
- allocate(sigma(0:ntyp1,0:ntyp1),r0(ntyp1,ntyp1)) !(0:ntyp1,0:ntyp1)
+ if (.not.allocated(sigma)) allocate(sigma(0:ntyp1,0:ntyp1))
+ allocate(r0(ntyp1,ntyp1)) !(0:ntyp1,0:ntyp1)
do i=1,ntyp1
do j=1,ntyp1
aa_aq(i,j)=0.0D0
bb_aq(i,j)=0.0D0
aa_lip(i,j)=0.0d0
bb_lip(i,j)=0.0d0
+ if (scelemode.eq.0) then
chi(i,j)=0.0D0
sigma(i,j)=0.0D0
r0(i,j)=0.0D0
+ endif
enddo
enddo
!--------------------------------
epslip(i,j)=epslip(j,i)
enddo
enddo
+ if (scelemode.eq.0) then
do i=1,ntyp
do j=i,ntyp
sigma(i,j)=dsqrt(sigma0(i)**2+sigma0(j)**2)
rs0(j,i)=rs0(i,j)
enddo
enddo
+ endif
if (lprint) write (iout,'(/a/10x,7a/72(1h-))') &
'Working parameters of the SC interactions:',&
' a ',' b ',' augm ',' sigma ',' r0 ',&
epsij=eps(i,j)
if (ipot.eq.1 .or. ipot.eq.3 .or. ipot.eq.4) then
rrij=sigma(i,j)
+ print *,"rrij",rrij
else
rrij=rr0(i)+rr0(j)
endif
bb_lip(i,j)=-sigeps*epsijlip*rrij
aa_lip(j,i)=aa_lip(i,j)
bb_lip(j,i)=bb_lip(i,j)
- if (ipot.gt.2) then
+ if ((ipot.gt.2).and. (scelemode.eq.0))then
sigt1sq=sigma0(i)**2
sigt2sq=sigma0(j)**2
sigii1=sigii(i)
!-----------------------------------------------------------------------------
subroutine read_general_data(*)
- use control_data, only:indpdb,symetr,r_cut_ele,rlamb_ele,ions
- use energy_data, only:distchainmax
- use geometry_data, only:boxxsize,boxysize,boxzsize
+ use control_data, only:indpdb,symetr,r_cut_ele,rlamb_ele,ions,&
+ scelemode,TUBEmode,tor_mode
+
+ use energy_data, only:distchainmax,tubeR0,tubecenter
+ use geometry_data, only:boxxsize,boxysize,boxzsize,bordtubetop,&
+ bordtubebot,tubebufthick,buftubebot,buftubetop
! implicit none
! include "DIMENSIONS"
! include "DIMENSIONS.ZSCOPT"
call reada(controlcard,'BOXX',boxxsize,100.0d0)
call reada(controlcard,'BOXY',boxysize,100.0d0)
call reada(controlcard,'BOXZ',boxzsize,100.0d0)
+ call readi(controlcard,"SCELEMODE",scelemode,0)
+ print *,"SCELE",scelemode
+ call readi(controlcard,'TORMODE',tor_mode,0)
+!C if(me.eq.king .or. .not. out1file .and. fg_rank.eq.0) then
+ write(iout,*) "torsional and valence angle mode",tor_mode
+
+ call readi(controlcard,'TUBEMOD',tubemode,0)
+
+ if (TUBEmode.gt.0) then
+ call reada(controlcard,"XTUBE",tubecenter(1),0.0d0)
+ call reada(controlcard,"YTUBE",tubecenter(2),0.0d0)
+ call reada(controlcard,"ZTUBE",tubecenter(3),0.0d0)
+ call reada(controlcard,"RTUBE",tubeR0,0.0d0)
+ call reada(controlcard,"TUBETOP",bordtubetop,boxzsize)
+ call reada(controlcard,"TUBEBOT",bordtubebot,0.0d0)
+ call reada(controlcard,"TUBEBUF",tubebufthick,1.0d0)
+ buftubebot=bordtubebot+tubebufthick
+ buftubetop=bordtubetop-tubebufthick
+ endif
ions=index(controlcard,"IONS").gt.0
call reada(controlcard,"R_CUT_ELE",r_cut_ele,15.0d0)
call reada(controlcard,"LAMBDA_ELE",rlamb_ele,0.3d0)
MPI_MIN,WHAM_COMM,IERROR)
call MPI_AllReduce(rgymax,rgymax_t,1,MPI_DOUBLE_PRECISION,&
MPI_MAX,WHAM_COMM,IERROR)
- potEmin=potEmin_t/2
+ potEmin=potEmin_t !/2 try now??
rgymin=rgymin_t
rgymax=rgymax_t
rmsmin=rmsmin_t
!#ifdef DEBUG
write (iout,*) wsc,wscp,welec,wvdwpp,wang,wtor,wscloc,&
wcorr,wcorr5,wcorr6,wturn4,wturn3,wturn6,wel_loc,&
- wtor_d,wsccor,wbond
+ wtor_d,wsccor,wbond,wcatcat
!#endif
do ib=1,nT_h(iparm)
!el old rascale weights
esccor=enetb(21,i,iparm)
! edihcnstr=enetb(20,i,iparm)
edihcnstr=enetb(19,i,iparm)
- ecationcation=enetb(42,i,iparm)
- ecation_prot=enetb(41,i,iparm)
+ ecationcation=enetb(41,i,iparm)
+ ecation_prot=enetb(42,i,iparm)
#ifdef DEBUG
- write (iout,'(3i5,6f5.2,14f12.3)') i,ib,iparm,(ft(l),l=1,6),&
+ write (iout,'(3i5,6f5.2,15f12.3)') i,ib,iparm,(ft(l),l=1,6),&
evdw+evdw_t,evdw2,ees,evdw1,ecorr,eel_loc,estr,ebe,escloc,&
- etors,etors_d,eello_turn3,eello_turn4,esccor
+ etors,etors_d,eello_turn3,eello_turn4,esccor,ecationcation
#endif
!#ifdef SPLITELE
! edihcnstr=enetb(20,t,iparm)
edihcnstr=enetb(19,t,iparm)
edihcnstr=0.0d0
- ecationcation=enetb(42,t,iparm)
- ecation_prot=enetb(41,t,iparm)
+ ecationcation=enetb(41,t,iparm)
+ ecation_prot=enetb(42,t,iparm)
do k=0,nGridT
betaT=startGridT+k*delta_T
projects / unres4.git / commitdiff