Dear gmx-users, I am trying to simulate coarse-grained dodecane using MARTINI force field. One of the properties I would like to measure is viscosity. I was trying to do this from NEMD (actually I am using Langevin stochastic dynamics) and I am facing the problem having negative(!) value for 1/eta calculated by g_energy. Am I missing something very obvious?
I am using 4.5.4 version. Thank you very much in advance. My .mpd file looks like: integrator = sd dt = 0.005 nsteps = 1000000 comm_mode = Linear nstcomm = 100 nstxout = 10000 ; write coords nstvout = 10000 ; write velocities nstfout = 0 ; write forces (Do not write them) nstxtcout = 0 ; write coords to xtc-trajectory file nstlog = 2000 ; print to logfile nstenergy = 100 ; print energies xtc_precision = 1000 xtc-grps = energygrps = DEC coulombtype = Shift rcoulomb_switch = 0.0 rcoulomb = 1.2 epsilon_r = 15 vdw_type = Shift rvdw_switch = 0.9 rvdw = 1.2 DispCorr = No tc-grps = DEC tau_t = 2.0 ref_t = 300 cos_acceleration = 0.1 Pcoupl = no gen_vel = no gen_temp = 300 gen_seed = 473529 ============================================= Dr Mikhail Stukan Schlumberger Dhahran Carbonate Research Center, Dhahran Techno Valley - KFUPM, P.O. Box 39011, Dammam / Doha Camp 31942, Kingdom of Saudi Arabia Tel: +966 3 331 6182 Fax:+966 3 330 0845 mstu...@slb.com<mailto:mstu...@slb.com>
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