On 2/28/13 12:22 AM, Anu Chandran wrote:
Dear users,
I am trying to do a coarse grained simulation of protein in water using
gromacs-4.6 with martini_v2.2 force field. While running grompp before npt
equilibration, I got a warning
"WARNING 1 [file npt.mdp]:
You are using pressure coupling with absolute position restraints, this
will give artifacts. Use the refcoord_scaling option."
By including "refcoord_scaling = com" in the mdp file, the equilibration
ran fine with out any errors or warnings.
The mdp file used is as shown below:
define = -DPOSRES
title = Martini
integrator = md
dt = 0.02
nsteps = 50000
nstcomm = 10
comm-grps = System
nstxout = 0
nstvout = 0
nstfout = 0
nstlog = 1000
nstenergy = 100
nstxtcout = 1000
xtc_precision = 100
xtc-grps = Protein
energygrps = Protein
nstlist = 10
ns_type = grid
pbc = xyz
rlist = 1.4
coulombtype = Shift
rcoulomb_switch = 0.0
rcoulomb = 1.2
epsilon_r = 15
vdw_type = Shift
rvdw_switch = 0.9
rvdw = 1.2
tcoupl = v-rescale
tc-grps = System
tau_t = 1.0
ref_t = 300
Pcoupl = Berendsen
Pcoupltype = isotropic
tau_p = 5.0
compressibility = 3e-4
ref_p = 1.0
gen_vel = no
gen_temp = 300
gen_seed = 473529
refcoord-scaling = com
constraints = none
constraint_algorithm = Lincs
unconstrained_start = no
lincs_order = 4
lincs_warnangle = 30
I would like to know whether the use of "refcoord-scaling = com" in the
mdp file is correct or not.
Yes.
-Justin
--
========================================
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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