AMBER Archive (2006)

Subject: Re: AMBER: Unstable RMS trajectory

From: Adrian Roitberg (roitberg_at_qtp.ufl.edu)
Date: Tue Oct 17 2006 - 12:41:31 CDT

Dave, Sonya wrote:
> It's RMSd. Sorry for being unclear.
> In case i'm misunderstanding something, this is what I do to plot:
>
> I make a text file cbs2on2_md2b.calcrms which contains
>
> trajin cbs2on2b_md2b.mdcrd
> rms first mass out cbs2on2b_md2b.rms time 0.1
>
> and then at the command line, I type:
> $AMBERHOME/exe/ptraj cbs2on2b_wat.prmtop < cbs2on2_md2b.calcrms
> xmgr cbs2on2b_md2b.rms
>
> Thank you for all the help.
>
> Sonya

There you go.
You are, at least, trying to compute rmsd for ALL atoms in your system,
including all water molecules, etc.
So this number must go up as water diffuses around your box and your
protein.

Please check the flags for mask under the rms commant in ptraj. 

-- 
                            Dr. Adrian E. Roitberg
                              Associate Professor
               Quantum Theory Project and Department of Chemistry

University of Florida                         PHONE 352 392-6972
P.O. Box 118435                               FAX   352 392-8722
Gainesville, FL 32611-8435                    Email adrian_at_qtp.ufl.edu
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