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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Received on Sun Jun 10 2012 - 23:30:02 PDT
