[gmx-users] compressed pbc box at the end of simulation - membrane protein with ligand
mark.j.abraham at gmail.com
Wed Jun 12 22:21:57 CEST 2019
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
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
and learn from their suggestions and the reasoning :-)
Thank you again.
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