Hi, If you want isotropic coupling, don't choose anisotropic. Otherwise, please make sure you read the documentation of the respective .mdp options.
Mark On Mon, Sep 12, 2016 at 5:54 PM Mohsen Ramezanpour < ramezanpour.moh...@gmail.com> wrote: > Hi Everyone, > > Please let me know your opinion on this question. Thanks in advance > > Mohsen > > On Wed, Sep 7, 2016 at 5:35 PM, Mohsen Ramezanpour < > ramezanpour.moh...@gmail.com> wrote: > > > Dear gromacs users, > > > > If we are interested in deformation in simulation box shape (*both angles > > and lengths*) during simulation for a lipid system, like what has been > > done in this article (fig 1, fig 2, and fig 3): > > > > "Phase behavior of a phospholipid/fatty acid/water mixture studied in > > atomic detail." > > http://www.ncbi.nlm.nih.gov/pubmed/16464104 > > > > > > Reading through Gromacs manual: > > > > "When the off-diagonal compressibility are set to zero, a rectangular > box will > > stay rectangular. Beware that anisotropic scaling can lead to extreme > > deformation of the simulation box." > > > > and discussions in forum like followings: > > > > https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx- > > users/2008-July/035341.html > > https://www.mail-archive.com/gmx-users@gromacs.org/msg31242.html > > http://gromacs.org_gmx-users.maillist.sys.kth.narkive.com/ > > kENAzgnS/pressure-coupling-for-anisotropic-system > > > > I am still in doubt of my .mdp file parameters. > > > > Considering that I want to apply a pressure of 1 bar to the lipid system, > > is it possible to catch the same box deformation? > > > > pcoupl = Parrinello-Rahman > > pcoupltype = anisotropic > > ref-p = 1.0 1.0 1.0 0.0 0.0 0.0 > > tau-p = 0.5 0.5 0.5 0.5 0.5 0.5 > > compressibility = 4.5e-5 4.5e-5 4.5e-5 4.5e-5 4.5e-5 > 4.5e-5 > > > > I chose ref-P as 0 for the last three values to not force the box to > change > > At the same time, I chose compressibilities and tau-p the same for all > > diagonal and non-diagonal values. > > > > Thanks in advance for your comments > > > > Thanks > > Mohsen > > -- > > *Rewards work better than punishment ...* > > > > > > -- > *Rewards work better than punishment ...* > -- > 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 gmx-users-requ...@gromacs.org. > -- 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 gmx-users-requ...@gromacs.org.
