Re: * CGtool force field *

From: HAMID - (h2a1385_at_gmail.com)
Date: Sun Oct 23 2011 - 03:09:03 CDT

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.
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.

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

Best.

On 10/23/11, Chris Harrison <charris5_at_gmail.com> wrote:
> 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
>>
>

-- 
----
H. Hadi
PhD student of Biophysics,
UT, Iran

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