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

Mark Abraham mark.j.abraham at gmail.com
Tue Oct 30 19:41:16 CET 2018


Your end point is a wildly different lipid configuration. Is such a
(phase?) transition expected?


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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