AMBER Archive (2008)

Subject: AMBER: nscm code

From: Naser Alijabbari (
Date: Fri Oct 10 2008 - 00:05:59 CDT


I have been looking at the sander source code folder for Amber 8 and I am
not recognizing any files that are about nscm or translation and rotation
removal. Can someone point out the file/files. I am trying to understand
what happens during translation and rotation removal during NVE ensemble
(eventhough it should not be necessary to do this). From the archive I
gather that for NVE (ntt not equal to 3) both translation and rotation are
removed. Also any article or books that would be a help in understanding the
code would be appreciated (I had a look at introductory books "Molecular
modeling" by Andrew Leach and "Computational chemistry" by Christopher
Cramer but did not recognize anything).

In the ptraj code I see the rms function but my C is very rusty so can
someone recommend source/sources for a better understanding.

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