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 - 21:00:02 PDT
