[gmx-users] SASA calculation for one replica in REMD

Simone Orioli simone.orioli at unitn.it
Tue Apr 23 11:11:08 CEST 2019


Hi,
I don't know if sasa calculations are implemented in gromacs. But if you
know a little bit of Python you can use MDTraj for that:

http://mdtraj.org/latest/examples/solvent-accessible-surface-area.html

or also Pymol:

https://pymolwiki.org/index.php/Get_Area

Cheers,
Simone

Il mar 23 apr 2019, 11:07 Shan Jayasinghe <shanjayasinghe2011 at gmail.com> ha
scritto:

> Dear Gromacs Users,
>
> I did replica exchange molecular dynamics simulation which contains 25
> replicas. Now I want to calculate the solvent accessible surface area of
> the surfactant (the first replica in my REMD) I used in my simulation at
> 298 K. How can I do that?
>
> Can anyone help me?
>
> Thank you.
> --
> 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