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

Mon Feb 29 09:30:05 CET 2016

Hi,

The simplest explanation for this is that one set of runs used position
restraints and one set did not.

Mark

On Mon, 29 Feb 2016 08:48 SAPNA BORAH <sapnauser365 at gmail.com> wrote:

> hi
> Thanks for the suggestion. I will give this a shot, and remove these
> restraints.
>
> I am unclear about what should I be looking in the log file as you
> mentioned. The conformations are not just close, they are the same as the
> initial conformation.
>
> I have some understanding on pbc that serves a problem in visualisation of
> the trajectory. I have applied the all sorts of pbc options, but somehow
> things are not falling into place.
>
> However the problem more grave here, for me, is the production run and the
> model stability that is happening throughout the simulations in different
> versions.
>
>
> Thanks.
> Sapna
>
> Sapna Mayuri Borah
> c/o Dr. A. N. Jha
> Research student
> Tezpur University,
> India
>
> On Mon, Feb 29, 2016 at 11:59 AM, Dries Van Rompaey <
> dries.vanrompaey at gmail.com> wrote:
>
> > Hi,
> > Looks like you might be applying positional restraints (define =-DPOSRES
> in
> > your mdp file). This is standard practice for equilibration, but I don't
> > think you want to be doing this for your production run, as this will
> > restrain your protein to conformations rather close to your starting
> > conformation. Check if this is the case in your logfile.
> >
> > Proteins coming 'out of the box' is caused by periodic boundary
> conditions.
> > This is probably not a problem. Read this for more information:
> >
> >
> http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions
> > Sometimes one pass of trjconv isn't enough to sort everything out and
> more
> > might be needed.
> >
> > Kind regards
> >
> > Dries
> > On 29 Feb 2016 5:25 a.m., "SAPNA BORAH" <sapnauser365 at gmail.com> wrote:
> >
> > > 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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