So you are saying that by slowly raising the temperature to 500K you did
not see unfolding,
but with REMD you did?
What are the timescales of each of these simulations?
It'd be a safe wager that your protein will unfold in MD at high
temperatures given enough time.
I recommend that if you use REMD you should use a much lower maximum
temperature and/or
backbone restraints to prevent unfolding.
On Fri, Jun 15, 2012 at 12:33 PM, Soumya Lipsa Rath <soumyalipsabt.gmail.com
> wrote:
> Sir,
>
> I was running a normal MD simulation which attained stability in a short
> period of time. Since I was expecting a particular change in the structure
> of my protein.. I ran a short equilibration and then gradually raised the
> temperature to nearly 500K and I could observe the changes within a short
> time.. During the MD run (in explicit solvent) I did not see any loss of
> secondary structure.. I had also ran a test simulation raising temperature
> from 300 to 310K in normal MD and I could see difference in the protein
> behavior, however, no secondary structure changes.
> I had asked this previously to the Amber users and people suggested me to
> use REMD. However, now I see that other domains of the proteins also
> undergo structural changes at the same temperature.
>
> Thanks
>
>
>
> On Fri, Jun 15, 2012 at 7:06 AM, 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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Received on Fri Jun 15 2012 - 02:30:03 PDT
