[gmx-users] protein unstable for parallel job while stable for serial one

Tsjerk Wassenaar tsjerkw at gmail.com
Tue Sep 19 15:07:23 CEST 2006

Hi Akansha,

Either you need to simulate both systems until you have full
convergence before you can make conclusions regarding the (dis)similar
behaviour or you have to test consistently, running replicate
simulations both on one processor and on 16.

That being said, it is very well possible that even between two
simulations of the same system under completely identical conditions,
except for the starting velocities and possibly the exact starting
structure, you will get two completely different results. If you're
protein can undergo a conformational change it's basically a matter of
chance whether you observe it or not.

Of course, I don't say it is not related to your simulation being
distributed over multiple processors. It may be, but in order to
exclude other effects you have to repeat simulations and/or work
through the code very carefully. Which version of Gromacs did you use?

Hope it helps,

On 9/18/06, Akansha Saxena <asaxena17 at yahoo.com> wrote:
> Hello
> Has anybody seen a protein becoming unstable on
> parallel nodes while remaining stable on single node?
> I am running a NPT molecular dynamics simulation. The
> system contains a protein with 141 residues surrounded
> by water making the total to 32714 atoms. I ran this
> simulation at two places for 8ns. One as a serial job
> and the other as a parallel job on 16 nodes.
> The protein remains stable all through for the serial
> job but for parallel job the protein  opens up after
> 3ns of simulation and is never stable after that.
> All other conditions are exactly the same. Any help
> would be highly appreciated.
> Akansha
> Akansha Saxena
> Graduate Student
> Department of Biomedical Engineering
> Washington University in St Louis
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Tsjerk A. Wassenaar, Ph.D.
Groningen Biomolecular Sciences and Biotechnology Institute (GBB)
Dept. of Biophysical Chemistry
University of Groningen
Nijenborgh 4
9747AG Groningen, The Netherlands
+31 50 363 4336

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