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

[SAPNA BORAH]

Dear Mark,

I have still not been able to solve my problem. A whole new problem has now
arisen. I am listing them as follows:

1. I am running 100ns simulations for 6 protein models and I was using both
version 4.6.5 and 5.0.4 when I found that after production run, my protein
models are behaving differently in both the versions. I am attaching the
images of rmsd differences in the link attached. Also, find the mdp files
attached used in both the versions.

2. I have run multiple runs for the models to see if there are changes, but
everytime, each of the models is very very stable and does not change in
conformation at all in 5.0.4 but does otherwise in 4.6.5.

3. There is another problem that the protein comes out of the water box in
4.6.5 and not in 5.0.4 in all the simulations. I have ensured to remove
jumps from the trajectories, make molecules whole.

Please help me in this regard.

http://dropcanvas.com/v0k0b

Regards,
Sapna.

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

On Thu, Feb 11, 2016 at 10:54 AM, Tsjerk Wassenaar <tsjerkw at gmail.com>
wrote:

> 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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