[gmx-users] Different results for same protein's simulation in 4.6.5 and 5.0.4
sapnauser365 at gmail.com
Thu Feb 11 05:27:37 CET 2016
Please find attached a plot showing the RMSD difference. It is for the same
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.
Sapna Mayuri Borah
c/o Dr. A. N. Jha
On Tue, Feb 9, 2016 at 1:07 PM, Mark Abraham <mark.j.abraham at gmail.com>
> 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.
> 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
> > 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
> > 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
> > --
> > Gromacs Users mailing list
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-request at gromacs.org.
> Gromacs Users mailing list
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
More information about the gromacs.org_gmx-users