[gmx-users] which chain to select for MD simulation

[bipin singh]

Sir,
You are right..I exactly mean the same as you interpreted....now I am clear.
Thanks a lot for your reply...
On Fri, Jul 8, 2011 at 13:26, felmerino at uchile.cl <felmerino at uchile.cl>wrote:

> Hey,
>
> I agree it was unclear, but i guess he meant that he has a crystal
> structure with two molecules in the asymmetric unit where he knows that the
> protein is a monomer in solution. Otherwise the question does not even make
> sense as you pointed out.
>
> If it is indeed the asymmetric unit thing, then of course starting from any
> of the two structures will give different resultsas they are two different
> startinf points. However, on the long term all the system properties should
> converge on the average. Anyways, you should obtain very similar results
> from any of the two structures.
>
> regards
>
> Felipe
>
>  ----Mensaje original----
> De: Mark.Abraham at anu.edu.au
> Fecha: 08-jul-2011 3:44
> Para: "Discussion list for GROMACS users"<gmx-users at gromacs.org>
> Asunto: Re: [gmx-users] which chain to select for MD simulation
>
>
> On 8/07/2011 4:52 PM, bipin singh wrote:
> > Hello,
> >
> > My protein have two identical chains A and B and the backbone rmsd
> > between the two chains is 0.33A.
> > My problem is that how to select(on what basis) one chain out of the
> > two for md simulation, whether the selection of one of the two
> > chains(A or B) will make any differences to the final results.
>
> Step back. Does it even make sense to use only one? Dimers are usually
> that way for a reason.
>
> Mark
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-- 
-----------------------
*Regards,*
Bipin Singh
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