Re: all-atom to coarse-grained system

From: Rabeta Yeasmin (
Date: Mon Feb 05 2018 - 11:23:20 CST

Dear Mr.Kwan and Marlin,

Thank you so much for your information. These are really helpful.
I have another question about protein structure. I am using a dimer
structure of protein inside lipid bilayer. There are hydrogen bonds and
some other interactions between the monomer. I am wondering if that will be
affected by coarse-graining simulation. I have seen in the
residue-based coarse-graining tutorial, they used some extra bonds to
compensate the interactions among the monomers in oligomer inside lipid
And also they
Rabeta Yeasmin

On Sat, Feb 3, 2018 at 2:04 PM, Marlon Sidore <>

> 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 <,+Chemin+Joseph+Aiguier&entry=gmail&source=g>
> 13402 cedex 20 Marseille
> France
> 2018-02-02 22:43 GMT+01:00 Rabeta Yeasmin <>:
>> 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 <> 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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