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, <[email protected]> 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 <[email protected]> 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! > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to [email protected]. > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to [email protected]. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to [email protected].
