[gmx-users] anisotropic pressure coupling
ramezanpour.mohsen at gmail.com
Thu Sep 8 01:35:58 CEST 2016
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
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:
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
*Rewards work better than punishment ...*
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