[gmx-users] anisotropic pressure coupling
ramezanpour.mohsen at gmail.com
Mon Sep 12 18:54:35 CEST 2016
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."
> 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 ...*
*Rewards work better than punishment ...*
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