Dear Mark ; The ./template dosn't have additional flags as shows below.The "-force" option dosn't work.
============================================================== =Option Filename Type Description =------------------------------------------------------------ = -s md.tpr Input Structure+mass(db): tpr tpb tpa gro g96 pdb = -f md.xtc Input Trajectory: xtc trr trj gro g96 pdb cpt = =Option Type Value Description =------------------------------------------------------ =-[no]h bool no Print help info and quit =-nice int 0 Set the nicelevel =-b time 0 First frame (ps) to read from trajectory =-e time 10 Last frame (ps) to read from trajectory =-dt time 0 Only use frame when t MOD dt = first time (ps) =-[no]w bool no View output xvg, xpm, eps and pdb files =-n int 1 Plot data for atom number n (starting on 1) =========================================================== Chuan > Date: Wed, 23 Jun 2010 18:40:36 +1000 > From: Mark Abraham <mark.abra...@anu.edu.au> > > You need to supply a trajectory that has forces, and then make the program > read the forces (probably with -force on the command line). Alternatively, > work through how the trajectory reading code works, and see how to set the > flags to make them read forces. > > Mark > > ----- Original Message ----- > From: è,é>ªå· <niexuech...@163.com> > Date: Wednesday, June 23, 2010 18:29 > Subject: [gmx-users] Problem of reading the atom'force from trr file using > template.c > To: gmx-users@gromacs.org > > > ----------------------------------------------------------- >>> Dear all, >> I am trying to analysis the force of a atom.So I change "fr.x[n][XX]" >> to "fr.f[n][XX]" in the template.c .But it turns up "Segmentation fault" >> .(The pointer "fr.f" is NULL) How could I get the force? > > > My mdp file: > > title = Yo >> cpp = /usr/bin/cpp >> constraints = all-bonds >> integrator = md >> dt = 0.002 ; ps ! >> nsteps = 2500000 ; total 5ns. >> comm_mode = NonE >> nstcomm = >> nstxout = 50 >> nstvout = 0 >> nstfout = 50 >> nstxtcout = 0 >> nstlog = 5000 >> nstenergy = 5000 >> nstlist = 10 >> ns_type = grid >> coulombtype =PME >> rlist = 1.4 >> rcoulomb = 1.4 >> rvdw = 1.4 >> pbc = xyz >> ; Berendsen temperature coupling is on in two groups >> Tcoupl = berendsen >> tc-grps = CNT SOL >> tau_t = 0.1 0.1 > ref_t = 300 300 >> ; Energy monitoring >> energygrps = CNT SOL >> ; Non-equilibrium MD > > freezegrps = CNP >> freezedim = Y Y Y >> ; Isotropic pressure coupling is now on >> Pcoupl = no >> ;Pcoupltype = isotropic >> ;tau_p = 0.5 >> ;compressibility = 4.5e-5 >> ;ref_p = 1.0 >> ; Generate velocites is off at 300 K. >> gen_vel = no >> gen_temp = 300.0 >> gen_seed = 537129 > > > Many thanks in advance, >> Chuan > > | > -----------------------------------------------------------
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