Dear gmx-users, 1) I am running simulation of two paracetamol molecules dissolved in supercritical CO2 in NVT ensemble. The problem is that the resulting temperature of the system is larger than the temperature specified in mdp file by ~ 20 K (i set ref_t = 410 K in mdp file). Berendsen and v-rescale thermostats behave similarly. The output from g_energy: " Statistics over 250001 steps [ 0.0000 through 500.0000 ps ], 1 data sets All statistics are over 2501 points Energy Average Err.Est. RMSD Tot-Drift ------------------------------------------------------------------------------- T-System 430.342 1.1 14.1796 6.30923 (K) "
2) When i run the same simulation but set 3 different subsystems (all CO2 molecules, the first paracetamol molecule, the second paracetamol molecule) coupled to different bathes with the same temperature, the resulting temperatures do not match the specified temperature = 410 K. The output from g_energy: " Statistics over 250001 steps [ 0.0000 through 500.0000 ps ], 4 data sets All statistics are over 2501 points Energy Average Err.Est. RMSD Tot-Drift ------------------------------------------------------------------------------- Temperature 428.82 1.2 14.356 -3.39055 (K) T-CO2 427.432 1.2 14.6848 -5.24 (K) T-PARA 452.434 3.7 91.2873 20.656 (K) T-PAR2 454.211 10 93.7436 37.8375 (K) " I would appreciate very much if someone gives me a hint what could be wrong. Thank you. Andrey ---- Andrey I. Frolov, PhD Postdoctoral fellow Institute of Solution Chemistry Russian Academy of Sciences Some information about system: There are 200 CO2 molecules, cubic box: 4 x 4 x 4 nm3. I set "coulombtype = Cut-off" just for testing purposes, PME gives similar results. Some mdp control options (for the 2) case): " ; RUN CONTROL PARAMETERS = integrator = md dt = 0.002 nsteps = 250000 comm-mode = Linear nstcomm = 1 ; NEIGHBORSEARCHING PARAMETERS = nstlist = 10 ns_type = grid pbc = xyz rlist = 1.1 ; OPTIONS FOR ELECTROSTATICS AND VDW = coulombtype = Cut-off rcoulomb = 1.1 vdw_type = Shift rvdw = 1.0 ; OPTIONS FOR WEAK COUPLING ALGORITHMS = tcoupl = v-rescale tc-grps = CO2 PARA PAR2 tau_t = 1.0 1.0 1.0 ref_t = 410 410 410 ; GENERATE VELOCITIES FOR STARTUP RUN = gen_vel = yes gen_temp = 410 gen_seed = 473529 ; OPTIONS FOR BONDS = constraints = hbonds constraint_algorithm = lincs unconstrained_start = no shake_tol = 0.00001 lincs_order = 4 lincs_warnangle = 30 morse = no lincs_iter = 2 "
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