Re: [AMBER] heavy atom rms

From: Thomas Cheatham III <>
Date: Wed, 5 Jan 2011 13:19:52 -0700 (Mountain Standard Time)

> #!/bin/csh
> ptraj file.prmtop <<EOF
> trajin
> rms first mass out spc_file.rms !.H= time 1.0
> When I run this file the plotted output (of spc_file.rms) is a smooth
> curve (it looks exponential) going from an rms of 0 at t=0 and
> approaching y = 40. There is no structure at all in the curve. I am
> enclosing the plot file (spc_file.rms).
> The rmsd curve for the alpha carbon atoms using a different ptraj script
> looks fine, giving me a plot that maximizes at about 1.5.

The ptraj output should provide a summary of the atom selection; check
this to see if you are selecting what you are expecting to select. The
curve is not perfectly smooth so it is measuring some change; perhaps you
are looking at the RMSd of solvent heavy atoms? These would rapidly rise
and plateau as waters exchange (until the correspondence between the
initial frame and later water positions is random?); in fact, I just
plotted this myself and get very similar results for a solvated system.

rms first mass out rms.wat :WAT.O


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Received on Wed Jan 05 2011 - 12:30:04 PST
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