[gmx-users] anisotropic pressure coupling

[Mohsen Ramezanpour]

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 ...*