you need to tell us more. by "implicitly", do you mean implicit
solvent? which one? what kind of structure distortions do you see? do
you see these in normal MD, or only when REMD is being used? at what
temperatures do they occur?
On Thu, Jun 7, 2012 at 11:58 PM, Soumya Lipsa Rath
<soumyalipsabt.gmail.com> wrote:
> Dear Amber Users,
>
> I am trying to run Replica exchange MD simulation implicitly. During the
> equilibration step and at higher temperatures, the structure of my protein
> becomes distorted. I have given the chirality restraints on the protein
> backbone. I wanted to know whether structural distortions at higher
> temperatures in normal or do I need to modify/add some parameters?
>
> Thanks,
>
> Soumya
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Received on Fri Jun 08 2012 - 03:30:04 PDT
