If the critical temperature of the protein is less than 400K (I'll guess it
is), this is what you should expect.
You should choose your temperature ladder appropriate to the type of
transitions you hope to see. If the
temperature is above the unfolding temperature.. it will probably unfold.
If you don't want to see such drastic transitions,
try an appropriately lower temperature. If you know exactly what you want
to move and what you don't you can use a high temperature
and apply structural restraints (such as harmonic restraints on the
Carbon-alpha RMSD).
-Dan
On Sat, Jun 9, 2012 at 1:10 PM, Soumya Lipsa Rath
<soumyalipsabt.gmail.com>wrote:
> 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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--
Dr. Daniel J. Sindhikara <http://goo.gl/fLAqx>
Ritsumeikan University <http://www.ritsumei.ac.jp/eng/> - Biwako Kusatsu
Campus <http://www.ritsumei.ac.jp/eng/html/about/abo_08.html/#kusatsu>
sindhikara.gmail.com
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Received on Sat Jun 09 2012 - 03:00:02 PDT
