On Fri, Jun 15, 2012 at 6:38 AM, Carlos Simmerling <
carlos.simmerling.gmail.com> wrote:
> I agree with you of course, but if it truly does not unfold at high T
> in normal MD, but does in REMD, this would suggest a bug. This is
> unlikely, though...
>
Or perhaps more rapid heating for the REMD simulations (IIRC, the OP heated
"normal MD" and "REMD" in different steps...)
>
> On Thu, Jun 14, 2012 at 9:36 PM, Daniel Sindhikara <sindhikara.gmail.com>
> wrote:
> > 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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> > --
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--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Fri Jun 15 2012 - 06:30:03 PDT
