He said that there is loss in secondary structure and domains are moving
apart which indicates unfolding.
This isn't a bug, just too high of a temperature.
On Fri, Jun 15, 2012 at 3:11 AM, Carlos Simmerling <
carlos.simmerling.gmail.com> wrote:
> can you explain more about where you found that it is stable in MD but
> not in REMD< using the same temperatures? this suggests a disturbing
> bug.
>
> On Mon, Jun 11, 2012 at 2:15 AM, Soumya Lipsa Rath
> <soumyalipsabt.gmail.com> wrote:
> > I am working with Cyclin Dependent Kinases, using ff99sb forcefield.
> > Simulation is run in implicit solvent, using igb=5. After raising the
> > temperature to 300K, the protein is subjected to multisander
> equilibration
> > using procedure similar to that in the tutorial. I don't want to study
> the
> > unfolding of protein but a specific loop movement which I assume is
> > restricted due to some energy barrier in normal MD simulation.
> >
> > Thanks
> >
> > On Sun, Jun 10, 2012 at 10:18 AM, Hai Nguyen <nhai.qn.gmail.com> wrote:
> >
> >> You need to give more detail like what your protein is, which force
> field
> >> you are using etc ... Do you know its melting temperature? Be specific
> as
> >> possible.
> >> Hai Nguyen
> >>
> >> 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 Thu Jun 14 2012 - 19:00:03 PDT
