[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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