[gmx-users] gromacs+CHARMM36+GPUs induces protein-membrane system collapse?
Ramon Guixà
ramonguixxa at gmail.com
Tue Oct 30 20:16:49 CET 2018
Hi Kevin,
I already changed all to h-bonds with no effect at all, but thanks for
pointing it out anyway.
Please download log and edr files from this link below:
https://drive.google.com/open?id=12DezJ9DEijlE1VKbWnu4-WDzHMqDpnKx
Ramon
On Tue, Oct 30, 2018 at 7:57 PM Kevin Boyd <kevin.boyd at uconn.edu> wrote:
> 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%
> > 7Cfdb86aab13ba44609edd08d63e98a944%7C17f1a87e2a254eaab9df9d439034
> > b080%7C0%7C0%7C636765222746307149&sdata=DM54p00ZnNqOS%
> > 2FXrqCf1ofo2DtqzACuFBJohZgzTViM%3D&reserved=0
> > > >
> > > > Many thanks in advance for the help!
> > > > --
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