[gmx-users] Number of Frames in Trajectory
varsha gautham
varsha.gautham88 at gmail.com
Fri Feb 13 09:38:19 CET 2009
Dear users,
Am trying to simulate a polymer in vaccum.But when i make the production run
and view trajectory(.trr) files in VMD am getting only one frame.Here's a
part of my mdp file:
title = polymer
cpp = /lib/cpp
constraints = all-bonds
integrator = md
dt = 0.005 ;
nsteps = 50000 ;
nstcomm = 1
nstxout = 1000
nstvout = 1000
nstfout = 1000
nstlist = 10
ns_type = grid
rlist = 1.0
rcoulomb = 1.0
rvdw = 1.0
; Berendsen temperature coupling is on in two groups
Tcoupl = berendsen
tau_t = 0.1 0.1
tc-grps = BEN NCH0
ref_t = 300 300
; Pressure coupling is not on
Pcoupl = no
tau_p = 0.5
compressibility = 4.5e-5
ref_p = 1.0
; Generate velocites is on at 300 K.
gen_vel = yes
gen_temp = 300.0
gen_seed = 173529
But the mdrun given for equilibriation step generated 96 frames.Is that
because of the algorithm that i specified in the integrtaor as MD.Because
other than md,when i gave bd or steep am getting more frames.So what is the
problem in obtining frames with "md" as input for integrator?
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