[gmx-users] refcoord-scaling option in CG

[Anu Chandran]

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.

Thank you,

with regards,
Anu