Hi Mark, Thanks for your reply.
I want anisotropic coupling because I want to have box shape deformation during simulation. Like what has been done in above mentioned article. I have read the manual already, but I am still in doubt. I am pretty sure it should be anisotropic to allow these deformations. Do you see anything wrong in parameters I have chosen? Please let me know. Cheers On Thu, Sep 15, 2016 at 4:10 AM, Mark Abraham <mark.j.abra...@gmail.com> wrote: > 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. > -- *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.