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

----------------------------------------------------------------------- The AMBER Mail Reflector To post, send mail to amber_at_scripps.edu To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu