A partial list. More were added since... Can be useful nevertheless... R
connect.f: program con
doing the connectivity
chain/chain.f: program chain
doing chain simulation
dynamics/dyna.f: program dynamics
doing dynamics
minimize/mini.f: program mini
doing energy minimization
pot/energy.f: program pote
calculating current POTential Energy
addbond.f: subroutine addbond(ubond)
add bonds to existing BULK
angtor.f: subroutine angtor()
make angles torson and improper torsions
angtor.f: subroutine pickup2(n, atom, arr1, arr2, out)
angtor.f: subroutine sort1(n, ra)
angtor.f: subroutine sort2(n, ra, rb)
angtor.f: subroutine sort4(n, ra, rb, rc, rd)
angtor.f: subroutine piksrt(n, arr)
dimer.f: subroutine dimer(ityp1,ityp2,mono_pt,updown,nprt,nbnd,iden,
joining two monomers:bonds, etc
fillpt.f: subroutine fillpt(ipart1,ityp1,ptnm_m1,id_m1,ib1_m1,ib2_m1
fill particles in BULK
getcrd.f: subroutine getcrd(ucrd,type)
read coordinates
getmoname.f: subroutine getmoname(name,imult,less,empty,copies
read monomer names from poly file
lego.f: subroutine lego(upoly,mono,nprt,mono_pt,nbnd,
top routine for ploymerization process
monomers.f: subroutine monomers(ucon,mono,nprt,mono_pt,nbnd,basenm,
read and organize mono file
overlap.f: subroutine overlap(x,y,z,x1,y1,z1)
overlap two structures for minimum mass weighted rms
pick.f: subroutine pick(ipick,ngrp)
pick.f: subroutine pick2(ipick,ngrp)
pick atoms (not working yet)
propert.f: subroutine prprt(uprm,basenm,basems,basechg,
read and organize property file
putcrd.f: subroutine putcrd(ucrd,type)
write coordinates (CHARMm format formatted)
rconn.f: subroutine rconn(urcon)
read connectivity file
search.f: subroutine srch_imp(indx1,indx2,indx3,indx4,i1,i2,i3,i4,
search for improper torsion in data_base
vcomprs.f: subroutine cmprs(vector,away,length)
compress one vector
vcomprs.f: subroutine cmprs2(vector1,vector2,away,length)
compress two vectors
vcopy.f: subroutine vdcopy(v1,v2,length)
copy double precision vector
vcopy.f: subroutine vicopy(v1,v2,length)
copy an integer vector
vcopy.f: subroutine vccopy(v1,v2,length,size)
copy a character vector
wconn.f: subroutine wconn(uwcon)
write connectivity file
chain/chndyn.f: subroutine chndyn(temp,tmpr,step,tfac,igrid,npri,nstep,nsvel,
do CHAIN dynamics
chain/comc.f: subroutine comc(r0,dmass,natom,pointr,
generate rigid body constraints
chain/crbm.f: subroutine crbm(r,scalar,sigma,grdcmx,grdcmy,grdcmz,
project out rigid body motion
chain/orthg.f: subroutine orthg(X,Y,n,amovr,sigma,n1,n2)
orthogonalize vectors with weight
chain/sds.f: subroutine sds(sener,dv,r,d0,e0,e1,bnbnd,bimag,nselec,pointr,
calculate derivative and energy of the whole chain
dynamics/getvel.f: subroutine getvel(uvel,type)
get velocity from coordinate file
dynamics/info.f: subroutine info(unit,jstep,nofreez,inofrz)
write info on dynamics progress
dynamics/picktemp.f: subroutine picktemp
pick multiple temperature (NOT WORKING YET)
dynamics/rdyncrd.f: subroutine rdyncrd(urcrd,ncoor,inofrz,nofreez)
read dynamics coordinate
dynamics/shake.f: subroutine shake(nc, ishak1, ishak2, dissq,
shake bonds (Not implemented yet)
dynamics/shakept.f: subroutine shakept()
dummy shake routine (not working yet)
dynamics/shakinit.f: subroutine shakinit(nofreez,inofrz)
initialize shake database (Not implemented yet)
dynamics/velinit.f: subroutine velinit(irand,tempi,ntemp,tpo)
initialize velocities from Boltzmann distribution
dynamics/wdyncrd.f: subroutine wdyncrd(uwcrd,nfrm,ncoor,inofrz,nofreez)
write CHARMm dynamics coordinate file
dynamics/wdynvel.f: subroutine wdynvel(uwvel,nfrm,nvelo,inofrz,nofreez)
write CHARMm dynamics velocity file
house.f: subroutine house
householder diagonalization routine
intrprtr/alert.f: subroutine alert(func,length1,message,length2,level)
Error messenger
intrprtr/brkpair.f: subroutine brkpair(exp1,l1,exp2,l2,special)
breaking pairs (used to read bonds)
intrprtr/echo.f: subroutine echo(sbr,sbrl,line,linel)
echoing command line
intrprtr/get4c.f: subroutine get4c(c4,empty)
get character*4 from command line
intrprtr/rline.f: subroutine rline(name,namel,unit)
read current command line
minimize/eforce0.f: subroutine eforce0(idim,xx,etotal,g)
initiate energy call from the minimizer
******THE PATH ROUTINES ARE NOT WORKING YET ****
path/pat17.f: subroutine PAT17(COMLYN,COMLEN,DS,ATOMPR,RW,EN,DC,WORK
pot/ebond.f: subroutine ebond()
bond energy
pot/eforce.f: subroutine eforce(cutoff)
top of energy routines
pot/eimphi.f: subroutine eimphi()
improper energy
pot/enonb.f: subroutine enonb()
van der Waals and electrostatic interactions
pot/ephi.f: subroutine etors()
torsion energy
pot/etheta.f: subroutine etheta()
angle energy
pot/exlist.f: subroutine exlist(l,m,flag)
sort and exclude those particles in exclusion list
pot/exlist.f: subroutine incl14(l,m,flag14)
1-4 list handler
pot/init_wre.f: subroutine init_wre(uwene,cutoff)
initiate energy output
pot/nbond.f: subroutine nbond(pointm,nblistm)
create atom neighbour list
pot/nbondm.f: subroutine nbondm(cutoff)
create monomer-monomer neighbour list
pot/wener.f: subroutine wener(uwene)
write energy to uwene file
of.f: function of()
Open File
search.f: integer function search(indx1,indx2,indx3,indx4,
search and match abgles or torsions against data-base
chain/hotchain.f: function hotchaf(vx,vy,vz,ptms,inofrz)
provide current temeprature of chain
dynamics/hot.f: function hot(vx,vy,vz,ptms,nofreez,inofrz)
provide current temeprature of dynamics
dynamics/velinit.f: function ran1(irand)
random number generator (poor one)
dynamics/velinit.f: function ran2(irand)
high quality random number generator
intrprtr/find.f: logical function find(expr)
if find expr in a line find=.true.
intrprtr/fopen.f: logical function fopen(unit)
if unit is opened fopen=.true.
intrprtr/getc.f: character*(*) function getc(expr,def,lcpext)
get a character with unspecified length
intrprtr/geti.f: integer function geti(expr,def)
get integer from expression in line
intrprtr/getr.f: function getr(expr,def)
get real number from expression in line
intrprtr/intgr.f: function intgr()
get the integer from next expression
intrprtr/number.f: function number()
get real number from next expression