[gmx-users] Pore Size

[Pierre Ghesquiere]

Hi !

I advise you to use the SURFNET program.

http://www.ebi.ac.uk/thornton-srv/software/SURFNET/

Cheers

-- 
P.

Le mercredi 19 octobre 2016 à 15:41 +0530, Sanket Ghawali a écrit :
>  Hi lists,
> 
> I have performed a md simulation of peptides in sds micelle for 100ns. The
> peptides move to the interface after a time interval of 30 ns and remains
> there till 100ns. After visualizing it in VMD i see a pore formation in sds
> near the interface where the peptide is. I also see water molecules
> entering the hole surrounding the peptide. I wish to calculate the pore
> depth.
> 
> Any suggestions on how to go about doing this?
> -- 
> Sanket