AMBER Archive (2005)

Subject: RE: AMBER: Is the MD simulation normal

From: Bill Ross (ross_at_cgl.ucsf.edu)
Date: Sun May 29 2005 - 12:04:01 CDT

> You have an average Ca-RMSD below 1.0A! This is an indication of a
> reasonable trajectory.

I overlooked the magnitude - yes, rmsd < 1.0 is very stable.

Very good comments by Yong.

> At the ns time scale, it is indeed a good idea to do more simulations
> and to run the simulations much longer. This way you can see a clear
> trend. You need to make sure you change the initial random number seed
> and do so just once at the beginning.

Also make sure that the random number generator is used, by choosing
the right option for initial velocities.

Bill
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