AMBER Archive (2006)

Subject: AMBER: Flag for removal of translational and rotational center-of-mass (COM) motion

From: Rajesh Murarka (raj_km97_at_yahoo.com)
Date: Wed Nov 08 2006 - 09:59:36 CST

Dear AMBER users,
 
 I have a quick question pertaining to the flag (NSCM) for the removal of translational and rotational center-of-mass (COM) motion. I'm doing the Langevin dynamics simulations (with GB/SA) of a peptide.
 
 As for this case NTB =0, the default value of NSCM=1000. However, to my knowledge, for the Langevin dynamics simulations, the translational COM should not remain constant and the rotational COM should fluctuate about zero. And I'm not sure what value should I use for NSCM?
 Could someone please help me out?
 
 Thanks a lot in advance,
 Rajesh
 
 
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