On 10/16/12 1:14 PM, Ali Alizadeh wrote:
Dear Justin
In your opinion, Why did not i get a symmetric results of number density?
The .mdp file does not give any really useful information for this problem,
except to show that you're using NPT, which I suspect might contribute to the
problem. Without plots and hard numbers, it's all hand-waving at this point.
-Justin
this is my md.mdp file:
title = OPLS
define = ;
; Run parameters
integrator = md ;
nsteps = 1000000 ;
dt = 0.001 ;
emtol = 10.0
emstep = 0.00001
; Output control
nstxout = 10 ;
nstvout = 10 ;
nstenergy = 10 ;
nstlog = 10 ;
nstxtcout = 10
xtc_precision = 10
; Bond parameters
continuation = no ;
constraint_algorithm = lincs ;
constraints = all-bonds ;
lincs_iter = 1 ;
lincs_order = 4 ;
; Neighborsearching
ns_type = grid ;
nstlist = 1 ;
rlist = 1.0 ;
rcoulomb = 1.0 ;
rvdw = 1.0 ;
; Electrostatics
coulombtype = PME ;
pme_order = 4 ;
fourierspacing = 0.16 ;
ewald_geometry = 3d
; Temperature coupling is on
tcoupl = berendsen ;
tc-grps = System ;
tau_t = 0.1 ;
ref_t = 240 ;
; Pressure coupling is on
pcoupl = berendsen ;
pcoupltype = isotropic ;
tau_p = 2.0 ;
ref_p = 300.0 ;
compressibility = 4.5e-5 ;
refcoord_scaling = com
; Periodic boundary conditions
pbc = xyz ; 3-D PBC
; Dispersion correction
DispCorr = EnerPres ;
; Velocity generation
gen_vel = no ;
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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