Hi Matthew,<br><br>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. <br><br>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. <br>
<br>cheers,<br>Itamar<br><br><div class="gmail_quote">On 18 August 2011 01:48, Matthew Zwier <span dir="ltr"><<a href="mailto:mczwier@gmail.com">mczwier@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
Could be a system blowing up, or perhaps a mis-compiled binary. What<br>
error messages do you get when the crash occurs?<br>
<div><div></div><div class="h5"><br>
On Tue, Aug 16, 2011 at 9:48 PM, Itamar Kass <<a href="mailto:itamar.kass@monash.edu">itamar.kass@monash.edu</a>> wrote:<br>
> Hi all GROMACS useres and developers,<br>
><br>
> 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.<br>
><br>
> Few of the things I had tried are:<br>
> 1. Running the simulations on different systems (OSX, linux or blue-gene).<br>
> 2. Using single or double precision versions.<br>
> 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.<br>
> 4. Running part of the equilibration stage as NVT and then switched to NPT.<br>
> 5. Started from different x-ray structures, with resolutions differ from 2.5 to 1.7 Angstrom.<br>
><br>
> 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.<br>
><br>
> All the best,<br>
> Itamar.<br>
><br>
><br>
><br>
><br>
><br>
><br>
><br>
</div></div>> -----<br>
> "In theory, there is no difference between theory and practice. But, in practice, there is." - Jan L.A. van de Snepscheut<br>
><br>
> ===========================================<br>
> | Itamar Kass, Ph.D.<br>
> | Postdoctoral Research Fellow<br>
> |<br>
> | Department of Biochemistry and Molecular Biology<br>
> | Building 77 Clayton Campus<br>
> | Wellington Road<br>
> | Monash University,<br>
> | Victoria 3800<br>
> | Australia<br>
> |<br>
> | Tel: +61 3 9902 9376<br>
> | Fax: +61 3 9902 9500<br>
> | E-mail: <a href="mailto:Itamar.Kass@monash.edu">Itamar.Kass@monash.edu</a><br>
> ============================================<br>
><br>
><br>
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</font></blockquote></div><br><br clear="all"><br>-- <br><br>-- <br><br><br>"In theory, there is no difference between theory and practice. But, in practice, there is." - Jan L.A. van de Snepscheut<br><br>===========================================<br>
| Itamar Kass, Ph.D.<br>| Postdoctoral Research Fellow<br>|<br>| Department of Biochemistry and Molecular Biology<br>| Building 77 Clayton Campus<br>| Wellington Road<br>| Monash University,<br>| Victoria 3800<br>| Australia<br>
|<br>| Tel: +61 3 9902 9376<br>| Fax: +61 3 9902 9500<br>| E-mail: <a href="mailto:Itamar.Kass@monash.edu">Itamar.Kass@monash.edu</a><br>============================================<br>