Sir,
Yes I meant implicit solvent. I followed the amber tutorial given in
http://ambermd.org/tutorials/advanced/tutorial7/ , using the same
equilibration input file (i.e., igb=5). When the temperature goes above
400K the secondary structure are getting lost and the protein domains are
moving apart. I don't see such structural changes in normal MD.
Thanks,
Soumya
On Fri, Jun 8, 2012 at 3:29 PM, Carlos Simmerling <
carlos.simmerling.gmail.com> wrote:
> 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 - 21:30:03 PDT
