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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