[gmx-users] anisotropic pressure coupling

Mark Abraham mark.j.abraham at gmail.com
Thu Sep 15 12:10:38 CEST 2016


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.mohsen at 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.mohsen at 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 ...*
> --
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