Re: all-atom to coarse-grained system

From: Rabeta Yeasmin (rabetayeasmin_at_gmail.com)
Date: Fri Feb 02 2018 - 15:43:57 CST

Dear Kwan,

Actually, I am looking for a convenient method to convert the whole system
and also give a better result for PMF calculation. I have reviewed the
residue-based coarse graining method. According to their tutorial, they had
first converted the protein-lipid system to coarse grain system and later
add ion and solvent. But my system has already water and ions in it, so I
am wondering if it is possible to convert the whole system to coarse-grain.
And another thing that in their lipid mapping file (martini-lipid.cgc),
they do not have POPS type lipid. But my system contains that kind of
lipid. I am not sure how to deal with that and also if I can use the same
file as in their tutorial files to correct for protein segments.

Thank you so much.

Rabeta Yeasmin

On Fri, Feb 2, 2018 at 2:03 PM, Victor Kwan <vkwan8_at_uwo.ca> wrote:

> Hi Rebeta,
>
> Before doing anything, think about how you define 'better'.
>
> Regards,
>
> Victor Kwan
>
>
> On 2/1/2018 4:29 PM, Rabeta Yeasmin wrote:
>
>> Dear NAMD users,
>>
>> I am trying to convert my all-atom umbrella sampling system containing
>> protein-lipid-water-ions into a coarse-grained system. I have already
>> prepared windows at different distances and equilibrated them using
>> all-atom simulation. I am wondering if I can continue the simulation from
>> there converting them into a coarse-grained system or I have to start
>> building system from the beginning.
>> I have seen two methods for converting all-atom simulation to
>> coarse-grained simulation in VMD CG tools plugin--residue based
>> coarse-graining (rbcg) and shape based coarse-graining (sbcg). I am
>> wondering which one will be better for my system.
>> I have tried in rbcg method, it has two .cgc files which convert protein
>> and water into the coarse-grained system. I am wondering how can I find cgc
>> file for lipid and other ions.
>>
>> Thanks.
>>
>> Rabeta Yeasmin
>>
>
>

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