[gmx-users] GROMACS 4.5.4 keep crashing all the time.

[Justin A. Lemkul]

chris.neale at utoronto.ca wrote:
> You'll need to provide a much better report than this if you want to 
> receive any useful help.
> 
> Copy and paste the exact commands of what you did
> Copy and paste the exact log file and error messages
> 

I'd also add that we need a detailed description of the system, including force 
field used and any other special considerations (distance restraints, modified 
parameters, etc).  An .mdp file would also be useful for the run that crashes.

-Justin

> Do this for 4.0.7 and 4.5.4, for which I trust that you have been using 
> exactly identical test systems. If not, then please try it again while 
> conserving the system.
> 
> Chris.
> 
> -- original message --
> 
> Hi Matthew,
> 
> Thanks for the reply. First, I don't thinks it is poorly compiled bin, as I
> used both GROMACS compiled by me (on my machine) or by the sys-admin on
> Linux cluster or blue-gene.
> 
> The simulations using 4.5.4 crashed giving LINCS error, which is not the
> case with 4.0.7 (using the same mdp and pdb files). Second, I don't thinks
> it is poorly compiled bin, as I used both GROMACS compiled with me (on my
> machine) or by the sys-admin on Linux cluster/blue-gene.
> 
> cheers,
> Itamar
> 
> On 18 August 2011 01:48, Matthew Zwier <mczwier at gmail.com> wrote:
> 
>> Could be a system blowing up, or perhaps a mis-compiled binary.  What
>> error messages do you get when the crash occurs?
>>
>> On Tue, Aug 16, 2011 at 9:48 PM, Itamar Kass <itamar.kass at monash.edu>
>> wrote:
>> > Hi all GROMACS useres and developers,
>> >
>> > I am interesting in simulating a small protein (~140 aa) in water, with
>> and without Ca ions. In order to do so, I had used version 4.5.4. I had
>> solvate the protein in water, add ions to naturalise the systems,
>> equilibrated the systems and then tried productive runs. Now, no 
>> matter what
>> I did, it crashed after few ps's of free MD or during the PR runs.
>> >
>> > Few of the things I had tried are:
>> > 1. Running the simulations on different systems (OSX, linux or
>> blue-gene).
>> > 2. Using single or double precision versions.
>> > 3. An equilibration stage, 1ns long with a time-step of 1fs, during 
>> which
>> the restrained forces where gradually reduced from 1000 to 50 kJ mol-1 
>> nm-2.
>> > 4. Running part of the equilibration stage as NVT and then switched to
>> NPT.
>> > 5. Started from different x-ray structures, with resolutions differ 
>> from
>> 2.5 to 1.7 Angstrom.
>> >
>> > Finally I had moved back to 4.0.7 which worked like charm. I wonder if
>> someone else had encounter something like this. Attached please find 
>> the mdp
>> files I used.
>> >
>> > All the best,
>> > Itamar.
>> >
>> >
>> >
>> >
> 
> 

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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