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.k...@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.k...@monash.edu > ============================================ > > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
