Hello,
Increasing the value of NRUN and adjusting NSTLIM accordingly can help.
After each NRUN for periodic systems as well, one can then remove these
motions. I am not aware of other alternatives.
-Sanjeev
On Thu, 25 Oct 2001, Michael G Cooney wrote:
Dear AMBER users,
I am interested in setting NSCM to periodically remove center of mass
motion to avoid a flying ice cube in a long MD simulation of a DNA-drug
complex in water, but according to the AMBER 5.0 manual this flag is
ignored in periodic simulations. Is there an alternative variable to set
to accomplish this? Also, will NSCM work with particle-mesh Ewald?
Also I am aware that NTT can be set to < 0 to reassign instead of
rescaling velocities, but have never seen an example of this (explicit) in
the literature.
Thanks for your help,
Michael G. Cooney
Postdoctoral Associate
Dept. of Chemistry
Georgia State University
Atlanta, GA 30303
Received on Thu Oct 25 2001 - 20:44:41 PDT
