VMD-L Mailing List

From: amin sagar (aamin.sagar_at_gmail.com)
Date: Tue Feb 13 2018 - 13:36:17 CST

Hi. You can directly make the coarse grained system using the Martini
Bilayer Maker feature of CHARMM-GUI. It allows using both POPS and POPG.

Amin.

On Wed, Feb 14, 2018 at 12:35 AM, Rabeta Yeasmin <rabetayeasmin_at_gmail.com>
wrote:

> 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
>>>
>>
>>
>