Re: [AMBER] cpptraj: rmsd problem

From: Daniel Roe <>
Date: Tue, 7 Jul 2015 08:20:17 -0600


I haven't been able to reproduce your problem. Here is my input (using
files that are part of the AmberTools cpptraj test suite):

parm tz2.truncoct.parm7
loadcrd 1 1 Frame1
loadcrd 1 1 Frame2
crdaction Frame2 translate x 1.0
crdout Frame1
crdout Frame2 append
rms first out rmsd.dat

rmsd.dat contains 0.0 for both frames, as expected. Without knowing how you
generated your trajectories or what input you are using I can only
speculate, but my guess is that you've maybe got some imaging going on with
your trajectory with PBC which is causing the translated frame to look
different than the first frame. If you would like, send me your topology
and trajectory files off-list and I will take a look at them.

On Tue, Jul 7, 2015 at 3:15 AM, Thomas Fox <> wrote:

> Whas is going on here? Is this a numerical problem of the RMSD routine
> for a
> large number of atoms ?

A 6700 water system + some solute is not a very big system. Cpptraj should
theoretically be fine handling systems containing ~2 billion atoms (or up
to the size of your memory, whichever comes first).

> PS. I use Amber14, cpptraj V14.01

You should update to the latest version which is 15 (that version doesn't
even have all the AT14 patches applied...)


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Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Tue Jul 07 2015 - 07:30:03 PDT
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