Re: [AMBER] algorithm for rms

From: Thomas Cheatham <>
Date: Fri, 17 Jun 2011 09:20:18 -0600 (Mountain Daylight Time)

> Does the code for rms align the center of mass or the geometric center
> before finding the optimum rotation matrix?

Yes. Both.

> How do I access the source code for rms so I can better understand what is
> happening and make changes?

The easiest way is to actually look at the source code directory:

<turretarch5 303> ls $AMBERHOME/AmberTools/src/ptraj/*.c
actions.c clusterLib.c display.c experimental.c io.c netcdf_ptraj.c pubfft.c second.c trajectory.c
analyze.c correlation.c energy.c help.c main.c parallel_ptraj.c rdparm.c thermo.c utility.c
cluster.c dispatch.c evec.c interface.c mask.c ptraj.c rms.c torsion.c

Note a file there named "rms.c". Alternatively, egrep for rms and see
all the files that refer to rms...

[The core functionality is in the rms() routine in rms.c; the "action"
which controls the call, i.e. determines whether to mass weight or not,
fit, etc. is in the routine transformRMS() in actions.c.


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Received on Fri Jun 17 2011 - 08:30:07 PDT
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