[gmx-users] gromacs+CHARMM36+GPUs induces protein-membrane system collapse?

[Ramon Guixà]

Hi Mark, thanks for the quick response

No transition expected, just pure POPC at 310K. In any case, I never saw
such box fluctuations during production before...

Any hint?

R

On Tue, 30 Oct 2018, 19:41 Mark Abraham, <mark.j.abraham at gmail.com> wrote:

> Hi,
>
> Your end point is a wildly different lipid configuration. Is such a
> (phase?) transition expected?
>
> Mark
>
> On Tue, Oct 30, 2018 at 7:24 PM Ramon Guixà <ramonguixxa at gmail.com> wrote:
>
> > Dear all,
> >
> > After several years simulating membrane proteins using GROMACS and the
> > CHARMM force field, I have come across this issue:
> > I use the CHARMM-GUI interface to prepare my membrane-protein system,
> that
> > I subsequently equilibrate using a standard protocol. However, after
> > several ns, namely 100 to 400 ns, systems become extremely unstable (i.e.
> > very large box fluctuations) until they eventually deform (i.e. membrane
> > abnormally enlarged, big water pores go through, and protein collapses).
> I
> > have tried several things, namely:
> >
> > 1 - I changed (increased/decreased) certain parameters within the mdp
> file
> > (e.g. tau-p).
> > 2 - I started from scratch, re-built and re-equilibrated the system.
> > 3 - I used different GROMACS versions, namely 5.4, gromacs2016 and
> > gromacs2018.
> > 4 - I used different computers and different GPUs.
> > 5 - I changed the system (other membrane proteins of the same family with
> > different ligands).
> >
> > Sooner or later (within 100-400 ns), same thing happens over and over
> again
> > in every protein-membrane system I simulate. Intriguingly, systems never
> > crash (i.e. simulations keep on running despite of the observed
> artifacts).
> > The only exception out of all tests so far happens upon running the
> system
> > using CPUs only. In the former test, I observe no fluctuations so far
> (500
> > ns).
> > I never came across this problem before using the same set-up, could it
> be
> > linked somehow to the updated version of the CHARMM force field
> > (CHARMM36m)? Any thoughts?
> > Please find below a link to a zip file with tpr, mdp, raw (skipped)
> > trajectory, init/end wrapped pdb files, and boxZ plot from one test,
> namely
> > one using gromacs 2018.3+GPU:
> > https://drive.google.com/open?id=1s3FWbk91danJW863BN-GqsgraSIore6D
> >
> > Many thanks in advance for the help!
> > --
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