Dear all, I have a problem using the pull code in Gromacs 4.5.1. I am running simulations with a small molecule at constrained distances from the bilayer center in a membrane (z-direction) in order to calculate permeability data. I use the force acting on the molecule (pullf.xvg) at different distances to calculate free energy profiles and diffusion coefficients. The problem I am facing is that the pull forces are fluctuating significantly more in version 4.5.1 compared to in 4.0.5. In 4.0.5 the forces normally fluctuate in the range of at most ±2000 kJ/mol/nm whereas in 4.5.1 they fluctuate in the range of at most ±50000 kJ/mol/nm. The average force is however similar in both versions, which results in reasonable calculated free energy profiles. However, the large fluctuations in forces make the autocorrelation function of the force different, and this causes problems when calculating diffusion coefficients. I have used the same mdp file as in version 4.0.5 with the difference that tau_t is increased from 0.1 to 0.4 (mdp file included below). The simulations are at least 7 ns. Is there anything trivial that I have missed when changing from version 4.0.5 to 4.5.1? I would really appreciate any help on this issue. Thanks in advance.
Regards, Emma The mdp file: title = x cpp = /lib/cpp include = define = integrator = md dt = 0.002 nsteps = 7500000 nstlog = 25000 nstenergy = 30 nstxout = 0 nstxtcout = 25000 nstvout = 0 nstfout = 0 xtc_grps = DPPC SOL X energygrps = DPPC SOL X nstlist = 10 ns_type = grid rlist = 1.0 coulombtype = PME rcoulomb = 1.0 vdwtype = Cut-off rvdw = 1.0 tcoupl = Nose-hoover tc-grps = DPPC SOL X tau_t = 0.4 0.4 0.4 ref_t = 323 323 323 Pcoupl = Parrinello-Rahman pcoupltype = semiisotropic tau_p = 1.0 1.0 compressibility = 4.5e-5 4.5e-5 ref_p = 1.0 1.0 gen_vel = yes gen_temp = 323 gen_seed = 173529 constraints = all-bonds pbc = xyz optimize_fft = yes unconstrained_start = no pull = constraint pull_geometry = cylinder pull_r1 = 1.0 pull_r0 = 1.5 pull_group0 = DPPC pull_group1 = X pull_vec1 = 0 0 1 pull_init1 = -0.006
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