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

felmerino at uchile.cl felmerino at uchile.cl
Fri Jul 8 09:56:02 CEST 2011


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.



----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.

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