Yes my system size is large i.e., total number of atoms is 10280...
Thanks
On Sat, Jun 2, 2012 at 9:19 AM, Hai Nguyen <nhai.qn.gmail.com> wrote:
> If your system size is too large for REMD run, you can try GB simulation
> (igb=7 or igb=8 is a good start). The sampling is much faster than in
> explicit solvent simulation due to lack of friction between solvent and
> solute.
>
> Hai Nguyen
>
> On Fri, Jun 1, 2012 at 7:15 AM, Soumya Lipsa Rath
> <soumyalipsabt.gmail.com>wrote:
>
> > Dear Amber Users,
> >
> > I am currently studying protein dynamics and was looking into a
> particular
> > loop movement in the protein. I had two different simulation
> temperatures,
> > at high temperature I could clearly observe the desired changes in the
> loop
> > within a short time frame of 10ns, however at 300K (i.e., room temp) even
> > after running for nearly 70ns, the structure remains relatively dormant,
> > with hardly any change. Can u please suggest some methods by which I can
> > overcome the current problem.
> >
> > Thanks in advance
> >
> > Soumya
> > **
> >
> > **
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Received on Fri Jun 01 2012 - 21:00:03 PDT
