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

Mark Abraham 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
> 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
and learn from their suggestions and the reasoning :-)


Thank you again.
> Regards.
> --
> Gromacs Users mailing list
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.

More information about the gromacs.org_gmx-users mailing list