----- Original Message -----
From: 聂雪川 <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
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|
> 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?
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
> > 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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