Re: [AMBER] Units for mass weighted covariance matrix in ptraj

From: Jason Swails <>
Date: Mon, 12 Jul 2010 22:56:23 -0400


Looking at rdparm.c, it appears as though the masses are read straight from
the topology file without any modification (since I don't see it multiplied
by any constant). The masses in the prmtop files are in atomic mass units
or g/mol. This is easy enough to verify, just by looking at the MASS
section of a prmtop file. You'll see lots of 1.401000E+01 (Nitrogen) and
1.201000E+01 (Carbon) and 1.008000E+00 (Hydrogen).

Hope this helps,

On Mon, Jul 12, 2010 at 9:34 PM, Lekpa Duukori <> wrote:

> Hi All,
> Please does anyone know the units for masses used in computing the mass
> weighted covariance matrix in Ptraj?
> Thanks.
> Lekpa
> _______________________________________________
> AMBER mailing list

Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
AMBER mailing list
Received on Mon Jul 12 2010 - 20:00:03 PDT
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