[gmx-users] trouble diagnosing a simulation that's blowing up (shake not converging --> segmentation fault)

Sat Jul 11 03:37:54 CEST 2015

Hi,

Sorry, I mean your [molecules] section. The order there, and the atom
orders looked up from [moleculetypes] imply the required atom ordering for
a matching .gro. Run grompp and see what it says.

Mark

On Sat, Jul 11, 2015 at 3:27 AM Nathan K Houtz <nhoutz at purdue.edu> wrote:

> 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.abraham at gmail.com>
> To: gmx-users at 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 <nhoutz at 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" <jalemkul at vt.edu>
> > To: gmx-users at 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" <jalemkul at vt.edu>
> > > To: gmx-users at 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
> >
> > jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> > http://mackerell.umaryland.edu/~jalemkul
> >
> > ==================================================
> > --
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