From: HAMID - (h2a1385_at_gmail.com)
Date: Wed Oct 26 2011 - 08:47:39 CDT
Excuse me for the delay in answering.
Thank you for reply. I would think more about the using of CG MD or
all atom MD in study two huge proteins complex.
On 10/24/11, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:
> 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.
>> I would appreciate your answer for my question, I think you know my
>> problem correctly and suggest a probable solution.
> 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.
-- ---- H. Hadi PhD student of Biophysics, UT, Iran
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