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

[Mark Abraham]

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