What's the difference between the two runs? Isolate which of the differences
makes your simulation run slow, and then the answer might present itself.
----- Original Message ----
From: sudheer <[EMAIL PROTECTED]>
To: gmx-users@gromacs.org
Sent: Monday, December 31, 2007 12:20:48 PM
Subject: [gmx-users] problem in pr.mdp file
hi gromacs users,
iam getting problem while doing postion restrian for the protein system
reunning very slow,
but i have done md.mdp for another system( bilayer-popc) its running normally,
whats the problem in my protein system?
i have used pr.mdp file like i am enlosing along with my mail
User spoel (236)
; Wed Nov 3 17:12:44 1993
; Input file
;
title = Yo
cpp = /usr/bin/cpp
define = -DPOSRES
constraints = all-bonds
integrator = md
dt = 0.002
nsteps = 25000
nstcomm = 1
nstxout = 50
nstvout = 1000
nstfout = 0
nstlog = 10
nstenergy = 10
nstlist = 10
ns_type = grid
rlist = 1.0
rcoulomb = 1.0
rvdw = 1.0
pbc = xyz
; Berendsen temperature coupling is on in two groups
; Pressure coupling is on
Tcoupl = berendsen
tc-grps = Protein SOL Na+
tau_t = 0.1 0.1 0.1
ref_t = 300 300 300
Pcoupl = parrinello-rahman
pcoupltype = isotropic
ref_p = 1
tau_p = 0.5
compressibility = 4.5e-5
; Energy monitoring
energygrps = Protein SOL Na+
; Generate velocites is on at 300 K.
gen_vel = yes
gen_temp = 300.0
gen_seed = 173529
41,1 Bot
3,1 Top
pls help me in this problem
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