VMD-L Mailing List

From: Rabeta Yeasmin (rabetayeasmin_at_gmail.com)
Date: Tue Feb 13 2018 - 13:05:15 CST

Dear Brian,

Thanks so much for your information. Charged lipids may be difficult, but I
have seen in some paper that they have worked on charged lipids using
coarse grain simulation . They had converted all-atom system to CG
structures using CG tools but I am not sure how they did that.

Thanks.

Rabeta Yeasmin

On Tue, Feb 13, 2018 at 10:31 AM, Brian Radak <brian.radak_at_gmail.com> wrote:

> 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
>>
>
>