[gmx-users] re: simulation-rigid
Mark.Abraham at anu.edu.au
Wed May 11 05:12:38 CEST 2011
On 05/11/2011 06:24 AM, Frank Neuhaus wrote:
> 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.
-------------- next part --------------
An HTML attachment was scrubbed...
More information about the gromacs.org_gmx-users