Justin A. Lemkul wrote: ; Berendsen temperature coupling is on in three groups > Tcoupl = berendsen > > tau_t = 0.1 0.1 0.1 tc-grps = protein sol NA+ > > ref_t = 300 300 300 > > Never couple solvent and ions separately. Surely grompp warned you that you > should be using "Protein Non-Protein"? See here: > > http://www.gromacs.org/Documentation/Terminology/Thermostats > > Hi Justin, thanks for the suggestion. Actually, it's an error I've always been doing and I'm glad I've solved it. However, I'm afraid it has nothing to do with the problem, because I just tried to run the MD again (after modifying the md.mdp as you told me) and the fatal error is still there. I've noticed the the T-coupling mistake is also in pr.mdp. Do you think that correcting it and re-running the PR simulation would fix the "water molecule can not be settled" problem? Anyway here is the pr.mdp (as it was before):
title = hsacyx warnings = 10 cpp = /lib/cpp define = -DPOSRES constraints = all-bonds integrator = md dt = 0.002 ; ps ! nsteps = 100000 ; total 200.0 ps. nstcomm = 1 nstxout = 250 nstvout = 1000 nstfout = 0 nstlog = 10 nstenergy = 10 nstlist = 10 ns_type = grid rlist = 0.9 coulombtype = PME rcoulomb = 0.9 rvdw = 0.9 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 6 ewald_rtol = 1e-5 optimize_fft = yes ; Berendsen temperature coupling is on in four groups Tcoupl = berendsen tau_t = 0.1 0.1 0.1 tc-grps = Protein SOL NA+ ref_t = 300 300 300 ; Pressure coupling is on Pcoupl = berendsen pcoupltype = isotropic tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocites is on at 300 K. gen_vel = yes gen_temp = 300.0 gen_seed = 173529 Thank you Simone Cirri
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