[gmx-users] refcoord-scaling option in CG

[Justin Lemkul]

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

========================================