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

[Itamar Kass (Med)]

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.
> >
> >
> >
> >
> >
> >
> >
> > -----
> > "In theory, there is no difference between theory and practice. But, in
> practice, there is." - Jan L.A. van de Snepscheut
> >
> > ===========================================
> > | Itamar Kass, Ph.D.
> > | Postdoctoral Research Fellow
> > |
> > | Department of Biochemistry and Molecular Biology
> > | Building 77 Clayton Campus
> > | Wellington Road
> > | Monash University,
> > | Victoria 3800
> > | Australia
> > |
> > | Tel: +61 3 9902 9376
> > | Fax: +61 3 9902 9500
> > | E-mail: Itamar.Kass at monash.edu
> > ============================================
> >
> >
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-- 

-- 


"In theory, there is no difference between theory and practice. But, in
practice, there is." - Jan L.A. van de Snepscheut

===========================================
| Itamar Kass, Ph.D.
| Postdoctoral Research Fellow
|
| Department of Biochemistry and Molecular Biology
| Building 77 Clayton Campus
| Wellington Road
| Monash University,
| Victoria 3800
| Australia
|
| Tel: +61 3 9902 9376
| Fax: +61 3 9902 9500
| E-mail: Itamar.Kass at monash.edu
============================================
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