Hi Chuan, in the template.c file is in the beginning the flag initialized:
int flags = TRX_READ_X; If you want to read out the forces you have to change this to, as: int flags = TRX_READ_F; in addition to changing fr.x to fr.f. Basti On Wed, 23 Jun 2010 20:00:27 +0800 聂雪川 <niexuech...@163.com> wrote: > 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 > > > | > > > ----------------------------------------------------------- -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
