VMD-L Mailing List

From: Brian Radak (brian.radak_at_gmail.com)
Date: Tue Feb 13 2018 - 10:31:47 CST

I have no specific knowledge of the coarse-graining capabilities in VMD,
but I do know that charged lipids are an extremely challenging application
for coarse-grained force fields (or at least Martini-like CG models). It's
very possible that no such recommendable force field exists.

HTH,
Brian

On Mon, Feb 12, 2018 at 5:32 PM, Rabeta Yeasmin <rabetayeasmin_at_gmail.com>
wrote:

> Dear VMD users,
>
> I am trying to set up an all-atom lipid-protein system in VMD and convert
> it to the coarse-grain system using the residue-based coarse-grain system.
> But VMD only have options to set up POPC and POPE lipid. But I need to set
> up POPS lipid or any kind of negatively charged lipid and a mixed system of
> two different lipids. I am wondering how can I do it.
> I know a way to set up membrane patch from CHARMM-GUI website. But I am
> afraid if there can be any problem using that structure to set up the
> system and convert it into the coarse-grain system.
>
> Thanks.
> Rabeta Yeasmin
>