varsha gautham wrote:
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
Are you sure you want positions, velocities and forces every thousand
steps? What are you going to do with the latter two? Check out the
manual, chapter 7.
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
Not possible - the above would generate at most 50.
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?
MD does MD, not energy minimization, as those others do.
Mark
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