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 -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
