[gmx-users] anisotropic pressure coupling

[Mohsen Ramezanpour]

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.abraham at 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.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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-- 
*Rewards work better than punishment ...*