Dear GROMACS users,
I want to simulate a system consisting of a plate modeled by atoms (5000 atoms) and a polyethylene chain (80 carbons). The plate is frozen and I am using tabulated potentials. In this system, the considered interactions are chain-chain and chain-plate. There are no electrostatic interactions. The system is placed in a box, with dimensions corresponding to the dimensions of plate and substantially larger height. My md.mdp file is as follows cpp = cpp define = integrator = md dt = 0.002 nsteps = 7500 nstcomm = 1 comm_mode = None nstxout = 10 nstvout = 10 nstfout = 10 nstxtcout = 10 nstlog = 10 nstenergy = 10 energygrps = Chain Plate freezegrps = Plate freezedim = Y Y Y energygrp_excl = Plate Plate energygrp_table = Chain Chain Chain Plate nstlist = 1 ns_type = simple rlist = 0.4 pbc = xyz vdw-type = User rvdw = 0.4 coulombtype = cut-off rcoulomb = 0.1 Tcoupl = nose-hoover tc-grps = System tau_t = 0.1 ref_t = 450 gen_vel = yes gen_temp = 450 constraints = none pcoupl = no After launching this job the process is running but there is no trajectory to be produced. The log file finishes in the section containing following information energygrp_flags[ 0]: 2 2 energygrp_flags[ 1]: 2 1 I have tried also running this job without user specified potential, with relaxed plate, with pbc=no and some other attempts, but I always failed in the same way. I would be very thankful for suggestions how to cope with this problem. Greetings Zuzana
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