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 <mczw...@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.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 > -- -- "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 ============================================
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