[gmx-users] anisotropic pressure coupling
mark.j.abraham at gmail.com
Thu Sep 15 12:10:38 CEST 2016
If you want isotropic coupling, don't choose anisotropic. Otherwise, please
make sure you read the documentation of the respective .mdp options.
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
> 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://firstname.lastname@example.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
> > I chose ref-P as 0 for the last three values to not force the box to
> > 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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