Justin A. Lemkul wrote:<br><br><blockquote style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;" class="gmail_quote">; Berendsen temperature coupling is on in three groups<br>Tcoupl = berendsen<br>
<br>tau_t = 0.1 0.1 0.1 tc-grps = protein sol NA+<br><br>ref_t = 300 300 300<br><br>Never couple solvent and ions separately. Surely grompp warned you that you should be using "Protein Non-Protein"? See here:<br>
<br><a href="http://www.gromacs.org/Documentation/Terminology/Thermostats">http://www.gromacs.org/Documentation/Terminology/Thermostats</a><br><br></blockquote><div><br>Hi Justin, thanks for the suggestion. Actually, it's an error I've always been doing and I'm glad I've solved it.<br>
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.<br>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?<br>
Anyway here is the pr.mdp (as it was before):<br><br>title = hsacyx <br>warnings = 10<br>cpp = /lib/cpp <br>define = -DPOSRES<br>constraints = all-bonds<br>
integrator = md<br>dt = 0.002 ; ps !<br>nsteps = 100000 ; total 200.0 ps.<br>nstcomm = 1<br>nstxout = 250<br>nstvout = 1000<br>nstfout = 0<br>
nstlog = 10<br>nstenergy = 10<br>nstlist = 10 <br>ns_type = grid<br>rlist = 0.9<br>coulombtype = PME<br>rcoulomb = 0.9<br>rvdw = 0.9<br>
fourierspacing = 0.12<br>fourier_nx = 0<br>fourier_ny = 0<br>fourier_nz = 0<br>pme_order = 6<br>ewald_rtol = 1e-5<br>optimize_fft = yes<br>; Berendsen temperature coupling is on in four groups<br>
Tcoupl = berendsen<br>tau_t = 0.1 0.1 0.1<br>tc-grps = Protein SOL NA+<br>ref_t = 300 300 300<br>; Pressure coupling is on<br>Pcoupl = berendsen<br>
pcoupltype = isotropic<br>tau_p = 0.5<br>compressibility = 4.5e-5<br>ref_p = 1.0<br>; Generate velocites is on at 300 K.<br>gen_vel = yes<br>gen_temp = 300.0<br>
gen_seed = 173529<br></div><br>Thank you<br><br>Simone Cirri<br>