Dear all,
1. I am performing MD simulation of a MARTINI coarse grained polymeric chains (named NGL in my mdp file below) in Coarse grained water (named W in mdp file below). 2. My equilibration and MD runs have been running perfectly until now. I have started doing NEMD simulations to get viscosity. The starting structure for NEMD came from an equilibrated system. 3. I am pretty sure that the error is in the mdp file. I am new to NEMD so it will be great if I can get some pointers of solving the issue. Is there a NEMD gromacs tutorial on the web? Here is the full mdp file for the NEMD run: title = Martini cpp = /usr/bin/cpp integrator = md tinit = 0.0 dt = 0.01 nsteps = 500 nstcomm = 1 comm-grps = system nstxout = 10 nstvout = 10 nstfout = 10 nstlog = 10 nstenergy = 10 nstxtcout = 2500 xtc_precision = 100 xtc-grps = energygrps = system nstlist = 1 ns_type = grid pbc = xyz rlist = 1.7 coulombtype = Shift rcoulomb_switch = 0.0 rcoulomb = 1.2 epsilon_r = 15 vdw_type = Shift rvdw_switch = 0.9 rvdw = 1.2 DispCorr = EnerPres tcoupl = V-rescale tc-grps = NGL W tau_t = 1.0 1.0 ref_t = 300. 300. Pcoupl = No Pcoupltype = Isotropic tau_p = 1.0 compressibility = 1e-5 ref_p = 1.0 gen_vel = Yes gen_temp = 300 gen_seed = 473529 constraints = None constraint_algorithm = Lincs unconstrained_start = no lincs_order = 1 lincs_warnangle = 30 ; Non-equilibrium MD stuff acc-grps = NGL W accelerate = 0.1 0 0 -0.1 0 0 freezegrps = freezedim = cos_acceleration = 0.1 deform = Best, SN Dr. Shikha Nangia 201D Chemistry Building Department of Chemistry The Pennsylvania State University University Park, PA 16802 Phone(o): 814-863-0289 Phone(cell): 612-599-9449
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