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

[Itamar Kass]

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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"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
============================================