[gmx-users] GROMACS 4.5.4 keep crashing all the time.
mczwier at gmail.com
Wed Aug 17 17:48:47 CEST 2011
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,
> "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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