[gmx-users] re: simulation-rigid

[Mark Abraham]

On 05/11/2011 06:24 AM, Frank Neuhaus wrote:
> Hi,
> I have a protein simulation in which all residues simulate correctly 
> with the exception of five in a loop.   These five out of 360 are in a 
> loop (or bend) separate from my area of interest.  Thus, I would like 
> to treat them as a rigid sequence.  Using the position restraints in 
> the posre.itp file does not help me.  I am looking for a script that I 
> can write into my mdp files that restricts all simulation in these 
> five residues.   Can anyone help me with this little issue?  Thank you.

What about their motion is not "correct"? If this is a disordered loop, 
then probably your reference data for these residues is less reliable 
than the MD simulation ensemble.

Mark
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