Thanks for the tip about the "blowing-up" page on the wiki--I already checked there and found little help because my crashes are coming so long into the runs (sometimes as late as 1 million steps in). This is also why I can't debug with nstxout = 1: the output files would get too big. I'm also reluctant to lower the time-step from 2 fs to say 1 fs, because I'm already resource-limited in these simulations, and slowing them down would halve the amount of sampling I could do.
Any other thoughts on this? The mdp file for these crashing runs is shown below: integrator = md nsteps = 2000000 dt = 0.002 nstlist = 10 nstcomm = 1 rlist = 1.0 coulombtype = pme rcoulomb = 1.0 vdw-type = cut-off rvdw = 1.0 tcoupl = Nose-Hoover tc-grps = protein non-protein tau-t = 0.5 0.5 ref-t = 298 298 nstxout = 1000 nstxtcout = 100 nstenergy = 100 > Message: 7 > Date: Fri, 31 Oct 2008 20:43:22 -0400 > From: "Justin A. Lemkul" <[EMAIL PROTECTED]> > Subject: Re: [gmx-users] Persistent crashes due to unsettled waters > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: <[EMAIL PROTECTED]> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > > > Aaron Fafarman wrote: >> Dear GMX-community, >> >> I'm running four related, equilibrium-dynamics simulations of a small >> protein in explicit water, each with a different non-natural >> amino-acid in the sequence. One of the four non-natural amino-acid >> containing proteins can be simulated for long times, up to 4 ns >> without incident, but the other three invariably crash. On repeated >> reinitialization (changing the box size, changing the duration of >> position restrained refinement) they still keep crashing at any time >> between 100's of picoseconds and 2 ns. Usually an error such as >> "3009.270 ps: Water molecule starting at atom 26883 can not be >> settled." is printed to the log file and the pdb of the step after the >> crash has nonsense numbers for the coordinates of the offending water >> molecule. It's always a different water molecule, always a >> high-numbered atom (>20000). The crashes happen on both a >> self-compiled linux build and on a self-compiled Mac OS 10.4 build, >> both GMX 3.3.1. A simulation of just the parameterized amino acids in >> a box of water never crashes over the course of a 4 ns simulation so I >> don't suspect my amino-acid parameters. > > As a general reference, check out the following: > > http://wiki.gromacs.org/index.php/blowing_up > > For debugging purposes, I have found that if I set nstxout = 1 in the .mdp > file, > I can usually capture the initial events leading to the explosion. > Unfortunately, the water molecule that cannot be settled is usually an > unfortunate victim of another molecule that has gone flying off across your > system. > > It might also be useful to post your .mdp file here if you are still unable to > find the problem. > > -Justin _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
