Re: all-atom to coarse-grained system

From: Vermaas, Joshua (Joshua.Vermaas_at_nrel.gov)
Date: Fri Feb 02 2018 - 15:55:35 CST

Why would a coarse grained system give more accurate PMF results? From what I've seen, Martini never makes the claim to be as good as atomic systems at describing energetics. It just claims to be good enough and useful for reaching timescales you couldn't get with an atomic system. If you want convenient methods of converting to a martini-type system, have you looked at martinize (http://cgmartini.nl/index.php/tools2/proteins-and-bilayers)?

-Josh

On 02/02/2018 02:48 PM, Rabeta Yeasmin wrote:
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<mailto: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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