From: HAMID - (h2a1385_at_gmail.com)
Date: Sat Oct 22 2011 - 14:11:14 CDT
Dear Dr. Kohlmeyer,
Thank you for your reply.
You are right about that I did not find any answer.
I should mentioned in my previous post that I checked all atom FF,
like charmm, for my issue but all atom MD was time consuming for me.
Thus I explored another method such as shape based and residue based
coarse graining methods. I decided to study the mechanical properties
of histone complex and initiation factor complex so I thought my
problem may have a solution via RBCG.
Maybe I did not express my idea about protein-protein complex clearly.
I decide to study the "sliding" of histone complex and initiation
factor complex on each other. ( I am informed of that a classical MD
package like NAMD is not able to reproduce QM calculations to study
About the cg water, I know the RBCG water bead represent a cluster of
water which contains four water molecules. In my first post about RBCG
water I asked about the polarizble CG water model like that the
martini polarizable water provides. I have tried several times to
translate martini polarizble water top and par file to CHARMM
counterpart but I could not reproduce a valid charmm like CG
polarizable water model yet. I hope I design a polarizable CG water
model for using in NAMD. So I ask every body to help me in this
Hope I have clarified that I did not complain about not getting any
answer. I have learned that I should study well and work hard to find
an answer. If I do not find reliable answer then I ask from experts
Excuse me if my questions seem not advanced. I am a beginner like any
I am still looking forward to hearing comments.
On 10/22/11, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:
> On Sat, Oct 22, 2011 at 1:00 PM, HAMID - <h2a1385_at_gmail.com> wrote:
>> Dear all,
>> I am looking forward to every one answer my previous post about RBCG
> dear hamid,
> if you don't get an answer, then usually for a reason.
> perhaps nobody thought that your question was
> worth answering, perhaps people thought the answer
> is too obvious, perhaps people didn't understand
> the question, perhaps nobody knows an answer.
> the remedy for each of these is that *you* have
> to think more about your problem, work harder
> and come up with a better/simpler question instead
> of complaining about not getting any. complaining
> only makes it _less_ likely to get a qualified answer.
>> 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
> pop quiz: what does a water bead in this model
> represent and what is the total charge of that?
>> model does not able to reproduce electrostatic interactions and I
>> think it is a disaster for my simulations.
> well, like the saying goes: if the cap don't fit, don't wear it.
>> 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)?
> this is a question that is best answered by studying
> the literature. it looks to me that you are very confused
> about what a coarse grain model can do and what not.
> it is pointless to study something that cannot be properly
> represented with a model you chose. you wouldn't want
> to use a classical force field to study bond breaking,
> or would you?
>> I would really appreciate any guide.
> my advice: get busy learning the method and its background
> before actually starting something that may be a waste of time.
>> H. Hadi
>> PhD student of Biophysics,
>> UT, Iran
> Dr. Axel Kohlmeyer
> akohlmey_at_gmail.com http://goo.gl/1wk0
> Institute for Computational Molecular Science
> Temple University, Philadelphia PA, USA.
-- ---- H. Hadi PhD student of Biophysics, UT, Iran
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