Re: all-atom to coarse-grained system

From: Marlon Sidore (marlon.sidore_at_gmail.com)
Date: Sat Feb 03 2018 - 14:04:34 CST

Hello,

You will not be able to convert the all atom water to CG water because of
the ambiguities in grouping water molecules. You will have to solvate the
system after.

For POPS or other lipids, you will need to update yourself the .cgc file.

Marlon

Marlon Sidore

PhD Student
Laboratoire d'Ingénierie des Systèmes Macromoléculaire (LISM)
CNRS - UMR7255
31, Chemin Joseph Aiguier
13402 cedex 20 Marseille
France

2018-02-02 22:43 GMT+01:00 Rabeta Yeasmin <rabetayeasmin_at_gmail.com>:

> 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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