AMBER Archive (2002)

Subject: Re: removing rotational motion

From: Andreas Svrcek-Seiler (svrci_at_tbi.univie.ac.at)
Date: Tue Feb 19 2002 - 06:27:18 CST

>
> I noticed that, in AMBER 6, the option for removing rotational and
> translational motion is no longer available.
>
> Am I mistaken? If not, is there an easy way to implement the removal of
> these motions.
... the sander manual says that this can be cotrolled using the NSCM and
NTCM flags.
As for doing it yourself:
Translation is easy: just calculate the COM velocity and subtract it from
the individual atom-velocities
Rotation is a little bit more work, but the details are most easily
obtained from textbooks about classical mechanics ( or e.g. from
the AMBER or TINKER sources).
good luck
andreas 

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