Re: * CGtool force field *

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Sun Oct 23 2011 - 16:16:47 CDT

On Sun, 2011-10-23 at 11:39 +0330, HAMID - wrote:
> Dear Chris,
>
> Thank you for your reply,
> Yes, you are right, I think my problem maybe solve via that model. (As
> I wrote in my previous posts at Oct 20, 2011 entitled by "RBCG
> electrostatic term", I seek CHARMM like MARTINI polarizable water.)
>
> I have started to add two dummy beads to a central water bead in RBCG
> water, I think I build a counterpart of MARTINI polarizable water. It
> works and the dummy particles get the orient based on the environment
> charge and dipole like Marrink work. But my polrizable model was slow.

this is to be expected. if you go from a 1-site to a 3-site
model, you increase the number of interactions that have to
be computed by a factor of 9.

if you add polarization treatment, it will have to be
even slower. at that point, you may find that it will
be simpler to run all-atom right away.

> I think I would work on the number of such water in a box. If you can
> help me to complete this model I will be glad to find your helps. I
> wonder if you check my model. Really I am ready to send it to you
> after some publishing.

as i mentioned before, the way to check it, is to compare
against the "original", i.e. use gromacs.

cheers,
    axel.

>
> I would appreciate your answer for my question, I think you know my
> problem correctly and suggest a probable solution.
>
> Best.
>

-- 
Dr. Axel Kohlmeyer
akohlmey_at_gmail.com http://goo.gl/1wk0
College of Science and Technology,
Institute for Computational Molecular Science,
Temple University, Philadelphia PA, USA.

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