VMD-L Mailing List

From: Rabeta Yeasmin (rabetayeasmin_at_gmail.com)
Date: Tue Feb 13 2018 - 13:36:35 CST

Thanks you so much.

Rabeta Yeasmin

On Tue, Feb 13, 2018 at 1:29 PM, Giacomo Fiorin <giacomo.fiorin_at_gmail.com>
wrote:

> You should contact the corresponding authors of that paper for this,
> rather than the mailing list.
>
> On Tue, Feb 13, 2018 at 2:05 PM, 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
>>>>
>>>
>>>
>>
>
>
> --
> Giacomo Fiorin
> Associate Professor of Research, Temple University, Philadelphia, PA
> Contractor, National Institutes of Health, Bethesda, MD
> http://goo.gl/Q3TBQU
> https://github.com/giacomofiorin
>