[gmx-users] Different results for same protein's simulation in 4.6.5 and 5.0.4

[SAPNA BORAH]

Dear Mark,

Please find attached a plot showing the RMSD difference. It is for the same
protein.

Even if the same runs are not reproducible, my doubt is whether there can
be such a large variation in the RMSD trend. Which data should I rely on
then, it is giving me a hard time.

I'll be grateful if you look into this.

Thanks,
Sapna.

Sapna Mayuri Borah
c/o Dr. A. N. Jha
Research student
Tezpur University,
India

On Tue, Feb 9, 2016 at 1:07 PM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> Hi,
>
> This is quite normal.
> http://www.gromacs.org/Documentation/Terminology/Reproducibility. You
> should see a similar range of variation in the trajectories produced in the
> two versions that are incompletely sampling the same ensemble, but one can
> say very little about two single observed trajectories sampled from them.
>
> Mark
>
> On Tue, Feb 9, 2016 at 8:23 AM SAPNA BORAH <sapnauser365 at gmail.com> wrote:
>
> > Dear all,
> >
> > I have tried running the same protein in the two versions of gromacs
> 4.6.5
> > and 5.0.4. Now, both the runs are producing entirely different results.
> >
> > The results till equilibration are same.
> >
> > After the run however, there is a total change in the production
> results. I
> > have used the same mdp files.
> >
> > I have rerun the systems and they still produce similar results in the
> same
> > version.
> >
> > The protein structure is a modelled one.
> >
> >
> > Thanks in advance.
> > Sapna.
> >
> > Sapna Mayuri Borah
> > c/o Dr. A. N. Jha
> > Research student
> > Tezpur University,
> > India
> > --
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