AMBER Archive (2007)Subject: Re: AMBER: rms and rmsf in ptraj
From: Scott Brozell (sbrozell_at_scripps.edu)
Date: Thu Mar 29 2007 - 09:57:43 CST
Hi,
On Wed, 28 Mar 2007, Thomas Cheatham wrote:
> > Can anybody tell me what's the difference between the two functions,
> > "rms" and "rmsf" in the file "rms.c" of ptraj program?
>
> Not much, although one of the routines has been updated more than the
> other (i.e. the one that is commonly called throughout ptraj)... One
> works in single precision (float) and the other works in double precision
> (double) if I remember correctly...
rmsf does not use the fit argument, but rms does:
< rms(int n, int mode,
---
> rmsf(int n, int mode,
< if (fit == 0) {
< /*
< * Don't do the fit, just calculate rmsd: don't calculate
< * any translation/rotation
< */
Also there is this difference in comments and presumably math:
< * First shift the center of mass of all the atoms to be fit to
< * the origin for both trajectory and reference coordinates.
---
> * First calculate CMs but don't really shift any coordinates
Scott
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