[gmx-users] anisotropic pressure coupling

[Mohsen Ramezanpour]

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 ...*