Re: * CGtool force field *

From: Chris Harrison (charris5_at_gmail.com)
Date: Sat Oct 22 2011 - 17:02:37 CDT

Hamid,

The Martini water particle doesn't carry a charge. From the martini parameter
file (http://md.chem.rug.nl/cgmartini/images/parameters/martini_v2.0.itp):

------------------------
;;;;;; WATER (representing 4 H2O molecules)

[ moleculetype ]
; molname nrexcl
  W 1

[ atoms ]
;id type resnr residu atom cgnr charge
 1 P4 1 W W 1 0

;;;;;; ANTIFREEZE (prevents freezing of water)

[ moleculetype ]
; molname nrexcl
  WF 1
                                                                                
[ atoms ]
;id type resnr residu atom cgnr charge
 1 BP4 1 WF WF 1 0
------------------------

Marrink and coworkers have developed a polarizable water model for the MARTINI forcefield, however its implementation in NAMD is not yet complete.

Perhaps such a polarizable RBCG model would solve the problems you're encountering?

Best,
Chris 

--
Chris Harrison, Ph.D.
Theoretical and Computational Biophysics Group
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801
char_at_ks.uiuc.edu                          Voice: 773-570-0329 
http://www.ks.uiuc.edu/~char              Fax:   217-244-6078
HAMID - <h2a1385_at_gmail.com> writes:
> Date: Sat, 22 Oct 2011 20:30:19 +0330
> From: HAMID - <h2a1385_at_gmail.com>
> To: namd-l <namd-l_at_ks.uiuc.edu>
> Subject: namd-l: * CGtool force field *
> 
> Dear all,
> 
> I am looking forward to every one answer my previous post about RBCG water.
> I check the RBCG water bead top and parameter file which implemented
> in CGtool folder of VMD.
> Again I see the water beads in RBCG have zero charge thus, such water
> model does not able to reproduce electrostatic interactions and I
> think it is a disaster for my simulations.
> Does any one introduce me a method to compensate the absence of water
> charge effects in my RBCG simulations (simulation of a huge protein
> complex - protein interactions)?
> I would really appreciate any guide.
> 
> Best.
> 
> ----
> H. Hadi
> PhD student of Biophysics,
> UT, Iran
>

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