[gmx-users] compressed pbc box at the end of simulation - membrane protein with ligand

[Mark Abraham]

Hi,

On Wed., 12 Jun. 2019, 07:47 Prasanth G, Research Scholar, <
prasanthghanta at sssihl.edu.in> wrote:

> Dear Bratin,
>
> Thank you for your prompt response. would using an isotropic pcoupletype
> have any effect on a membrane protein simulation?
>

It will keep the box vectors in the same ratio, yes... hence isotropic.

If we provide same ref_p values for all three axis (as in the above case)in
> a semiisotropic treatment, would this have the same effect as isotropic
> treatment?
>

No. Semiisotropic permits one set of dimensions to get larger while the
others get larger to a different extent (or even smaller). Not the same.

I would be grateful if anyone can share the template of the mdp files for a
> membrane protein simulation.
>

I suggest you check out
https://www.livecomsjournal.org/article/5966-simulation-best-practices-for-lipid-membranes-article-v1-0
and learn from their suggestions and the reasoning :-)

Mark


Thank you again.
> Regards.
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