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

[Tsjerk Wassenaar]

Hi Sapna,

The list doesn't allow attachments. Please put them somewhere online and
provide a link.
The differences can be large. Can't tell if you don't know the possible
range of conformations/trajectories for one Gromacs version.
Did you ensure to remove jumps from the trajectories and/or make molecules
whole, etc? That would be the only thing we'd be able to see from the RMSD
plot anyway, whether you removed jumps or not. Otherwise it does not
contain useful information (in this regard).

Cheers,

Tsjerk
On Feb 11, 2016 05:28, "SAPNA BORAH" <sapnauser365 at gmail.com> wrote:

> 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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