[gmx-users] lipid bilayer simulation-simulation setup

Mohsen Ramezanpour ramezanpour.mohsen at gmail.com
Tue Jan 2 17:00:17 CET 2018

Hi Gormacs users,

I was wondering if you have any opinion regarding these questions?

Thanks in advance for your comments

On Fri, Dec 29, 2017 at 5:55 PM, Mohsen Ramezanpour <
ramezanpour.mohsen at gmail.com> wrote:

> Hi Everyone,
> Lipid bilayers are (almost all the times) simulated in a rectangular or
> cubic boxes where all the angles are 90 between the PBC box sides. They are
> usually equilibrated with semi-isotropic Berendsen P-coupling whereas the
> production runs use semi-isotropic Parrinello-Rahman p-coupling (this part
> make sense). I have two questions:
> 1) What is the problem if we use a triclinic box with 90 90 120 angles for
> bilayer simulation:
> If we choose the z-direction as the normal vector to the bilayer. and a
> semi-isotropic p-coupling will be applied to the XY plane?
> 2) There are some publications who used the Berendsen coupling for
> production run as well. They do not usually explain why they prefer this
> barostat for the production run. It is known that Berendsen barostat is not
> producing the target ensemble as good as Parrinello-Rahman.
> It might be, however, because of using anisotropic p-coupling where both
> the box sides lengths and angles are allowed to change.
> Any idea?
> Thanks in advance for your input on this questions.
> Cheers,
> Mohsen
> --
> *Rewards work better than punishment ...*

*Rewards work better than punishment ...*

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