VMD-L Mailing List

From: Raman Preet Singh (ramanpreetsingh_at_hotmail.com)
Date: Fri Dec 18 2020 - 11:50:00 CST

Dear John and Peter,

Thank you very much for the clarification.

Regards,
RPS

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________________________________
From: Peter Freddolino <petefred_at_umich.edu>
Sent: Friday, December 18, 2020 11:06:08 PM
To: John Stone <johns_at_ks.uiuc.edu>; Raman Preet Singh <ramanpreetsingh_at_hotmail.com>; vmd-l_at_ks.uiuc.edu <vmd-l_at_ks.uiuc.edu>
Subject: Re: vmd-l: SBCG of molecules

I can just add -- SBCG is a completely different paradigm from the way MARTINI works, so the question is not really applicable. Please see the SBCG paper for how this method works. RBCG can be used with current MARTINI versions or any MARTINI-like model by making different .cgc files.
Best,
Peter

On Fri, Dec 18, 2020 at 12:29 PM John Stone <johns_at_ks.uiuc.edu<mailto:johns_at_ks.uiuc.edu>> wrote:
I believe that both the residue- and shape-based coarse graining tools
were developed when only the the earliest version of MARTINI had existed.
Whatever capabilities they may have with regard to MARTINI specifically
are likely now out of date. Those two tools have not been revised in
many years. They were developed and contributed by students and have
been "as-is" since then.

Best regards,
  John Stone

On Sat, Dec 12, 2020 at 06:29:43PM +0000, Raman Preet Singh wrote:
> Dear All,
> I am using MARTINI CG for membrane simulations. RBCG can build MARTINI
> compatible CG models. Does SBCG also build MARTINI compatible CG models?
> If not, is there a way to get MARTINI compatible CG models from SBCG?
> Regards,
> Raman 

--
NIH Center for Macromolecular Modeling and Bioinformatics
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University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
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