[gmx-users] Inconsistent results in different clusters and cores

tarak karmakar tarak20489 at gmail.com
Sun May 12 19:34:44 CEST 2013

Thanks Justin for the Quick and Helpful reply.

   Yes. If I am right, the chaotic behavior of the simulations is inherent
and can be assessed statistically by generating several independent
trajectories and analyzing their similar outcomes. But with the same '.mdp'
file I am getting TOO much different results, and that's where I worry.
I'll surely try with the recent version of gromacs. But, for now, can you
give me a little more informations about problems (bugs) with the 4.5.5
version, related to my context?


On Sun, May 12, 2013 at 10:55 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

> On 5/12/13 1:17 PM, tarak karmakar wrote:
>> Dear All,
>>       I am simulating a protein in water to check the ligand movement
>> over a
>> time span. I have    minimized the system in STEEP and CG and after that
>> heated from 0K - 300K within a time span of 300 ps. Then, I performed the
>> NPT production runs. In two clusters I have got different results, like in
>> one I see the ligand came out of the protein and in other it stayed inside
>> the protein cavity, after a same (comparable) time duration. Now, while
>> running the same job (same .mdp file) in different numbers of cores (in
>> the
>> same machine) I'm getting different behaviors, e.g., in protein ligand
>> distance plots etc. I don't know the reason behind this. I'm running all
>> my
>> jobs in gromacs-4.5.5 version.
>>       Recently I have visited this post [
>> http://redmine.gromacs.org/**issues/1012<http://redmine.gromacs.org/issues/1012>], but could not able to conclude
>> properly. Anyone's help would be greatly appreciated.
> I don't know if that issue is related, but if it is, then you're using an
> affected version (4.5.5).  Run again using the latest version (4.6.1) and
> see if the problem persists.  Realize too that MD simulations are chaotic,
> and there is no guarantee that one trajectory will be identical to another.
>  In principal, on average, multiple trajectories should produce similar
> behavior.  If you think that core count is a problem, run with mdrun
> -reprod to see if any optimizations are causing issues.  Build a solid test
> case, one that eliminates the possibility that your ligand topology is
> inaccurate.
> -Justin
> --
> ==============================**==========
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
> ==============================**==========
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