[gmx-users] gromacs+CHARMM36+GPUs induces protein-membrane system collapse?
Kevin Boyd
kevin.boyd at uconn.edu
Tue Oct 30 19:57:05 CET 2018
Hi,
Can you send an edr and log file?
I believe your constraints are nonstandard, iirc for charmm36 constraints
should just be h-bonds, but I doubt that would cause this.
Kevin
On Tue, Oct 30, 2018 at 2:50 PM, Ramon Guixà <ramonguixxa at gmail.com> wrote:
> 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://na01.safelinks.protection.outlook.com/?url=
> https%3A%2F%2Fdrive.google.com%2Fopen%3Fid%3D1s3FWbk91danJW863BN-
> GqsgraSIore6D&data=02%7C01%7Ckevin.boyd%40uconn.edu%
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> > >
> > > Many thanks in advance for the help!
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