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 Thu Jun 14 2012 - 21:00:02 PDT
