Hi, Thanks Mark. I'm sorry though, I don't think I understand what you mean. I thought the [system] section of the topology file was just a name for the system. How should I imply an order for the atoms? I did double check that the ordering in atoms is the same as it is in my .gro file (grommp -c input). 'OW', 'HW', 'HW', then 'DW'
----- Original Message ----- From: "Mark Abraham" <mark.j.abra...@gmail.com> To: gmx-us...@gromacs.org Sent: Friday, July 10, 2015 7:24:49 PM Subject: Re: [gmx-users] trouble diagnosing a simulation that's blowing up (shake not converging --> segmentation fault) Hi, That could only happen if your grompp -c input used a different atom ordering from that implied by your [system] section of your .top. grompp warns about this, but maybe you didn't notice... (Or the structure you loaded into VMD is a mismatch to the trajectory, so its heuristics for guessing where bonds actually are get double-crossed.) Mark On Sat, Jul 11, 2015 at 1:15 AM Nathan K Houtz <nho...@purdue.edu> wrote: > Actually, I think I found the problem. When i looked at the pdb files in > vmd the first time I missed it, but a colleague had a hunch and I found > that he was right! I think that shake is constraining atoms to the wrong > molecules. Here's a screenshot I took where you can see what I mean: > http://imgur.com/1bgThDv > > I'm still not sure how to fix it though. The molecule numbering in my .gro > file is correct, and there are only 4 atoms per molecule (or 3 plus the > dummy). How can I tell shake to look at each molecule individually? Or have > I made a mistake somewhere? Here are my most recent files: > > .gro file: (only part of it -- there is a character limit. this is the > first and last ten molecules with the box dimensions at the bottom) > http://textuploader.com/e898 > > topology file: > http://textuploader.com/e89g > > minimization: > http://textuploader.com/e8rc > > .mdp file: > http://textuploader.com/e896 > > log file from a failed simulation: > http://textuploader.com/e80y > > Thanks for your help! If you do still want the full .gro file to run the > simulation, I can look for a different file host. > Nathan > > > ----- Original Message ----- > From: "Justin Lemkul" <jalem...@vt.edu> > To: gmx-us...@gromacs.org > Sent: Friday, July 10, 2015 5:06:34 PM > Subject: Re: [gmx-users] trouble diagnosing a simulation that's blowing up > (shake not converging --> segmentation fault) > > > > On 7/9/15 9:23 PM, Nathan K Houtz wrote: > > Thanks for your explanations, Dr. Lemkul. > > > > I had already corrected a couple of the things you suggested. Gromacs > won't actually let me run with Nose-Hoover and Parrinello-Rahman together > (or at least, it gives a warning not to do that and stops). I'd like to run > in NVT anyway, so I had set Pcoupl to 'no'. I had also increased the > cutoffs and my nstlist is 20. > > > > I have now also changed the tcoupl to v-rescale, but unfortunately that > alone didn't help. So I'm not sure exactly what I can inspect to find the > source of my error. I know that temperature, pressure, and total energy are > all warning signs of bad things if they misbehave, but they were all fairly > constant throughout the simulation. (This is for the flexible-model > simulation:) The starting energy for 1700 water molecules at 120K was > -1.08744e+05, and it finished at -1.06047e+05 with no significant > variations on any step. Pressure and temperature were also fine. I > attempted to look at the results visually in vmd but I might have done > something wrong because the .trr file has some error in it and vmd crashes. > But the starting geometry after minimization looks fine: none of the > molecules were moved out of their position in the crystal. > > > > For the constrained molecules, the energy stays about the same (about > -1e+5) for the first 8 timesteps and then quickly blows up to +2e15 at step > 12 before it obviously fails. I get shake warnings from step 0 though. In > vmd, the first 8 steps look reasonable (checking the .pdb files that > gromacs outputs when there are warnings) and all the molecules seem to hold > their places in the crystal, but then at step 9 suddenly some of the > molecules become misshapen with very long or very short bonds. Of course it > goes downhill from there, but I can't figure out what's causing the > problems since it's clearly happening from the very beginning (according to > the shake warnings). > > > > What other things could I look at to troubleshoot my problem? > > > > Not sure, but at least the failure happens fast. Upload all your input > files > somewhere and I'll take a few minutes to see if I can spot anything. > > -Justin > > > Thanks for your help, > > Nathan > > > > ----- Original Message ----- > > From: "Justin Lemkul" <jalem...@vt.edu> > > To: gmx-us...@gromacs.org > > Sent: Thursday, July 9, 2015 7:39:47 AM > > Subject: Re: [gmx-users] trouble diagnosing a simulation that's blowing > up (shake not converging --> segmentation fault) > > > > > > > > On 7/8/15 8:06 PM, Nathan K Houtz wrote: > >> Hello, > >> > >> I deleted the email and can't respond to my last reply directly - > sorry! I > >> got this response from Mark Abraham: > >> > >> Hi, Try doing some EM and initial equilibration with no constraints at > all, > >> perhaps? Mark > >> > >> I tried commenting out the shake commands, and got a short (5000 step) > >> simulation to run just fine without blowing up. Before, I would get > shake > >> warnings from the first few steps and a segmentation fault around step > 13 or > >> 14. I would like to be able to simulate with rigid molecules, though. > Why > >> would the simulation work with flexible molecules but not rigid ones? > >> > > > > Flexible water allows weird geometry, which is probably coming up and > causing > > your constraint algorithm to fail. I'd inspect the outcome carefully. > Just > > because it runs doesn't mean it's right. > > > >> Also, in the example .mdp file for tip4p water, there is the (outdated) > >> option, 'unconstrained-start', which is now 'continuation'. I got > errors when > >> trying to make the input .tpr file when I attempted to set that option > to > >> 'yes'. The warning said it was because I want Gromacs to generate > velocities > >> to start the simulation, which is incompatible with that command. Is > there > >> another way I can try to start the simulation unconstrained? Or would > you > >> suggest another idea to fix my shake warnings? > >> > > > > What this setting says is "have the constraints already been solved > > (continuation = yes) or should mdrun constrain the starting > configuration itself > > (continuation = no)." > > > > The .mdp file has a number of weird settings. I would never use > Nose-Hoover and > > Parrinello-Rahman when generating velocities; that's likely to be very > unstable. > > See if a more forgiving thermostat and/or barostat resolves the > issue, e.g. > > tcoupl = v-rescale and pcoupl = Berendsen. > > > > Also note that the cutoffs are very short (probably because they want to > use a > > small box, but note that it *does* affect the physics) and nstlist = 1 is > > totally unnecessary. It doesn't hurt your physics, but it's a major > waste of > > performance. > > > > -Justin > > > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Ruth L. Kirschstein NRSA Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 629 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > http://mackerell.umaryland.edu/~jalemkul > > ================================================== > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? 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