Re: [AMBER] rmsd calculations on multiple trajectories

From: Daniel Roe <>
Date: Fri, 29 Jul 2016 08:31:56 -0600


On Fri, Jul 29, 2016 at 6:26 AM, Hirdesh Kumar <> wrote:
> rms A first :1-88.C,CA,N rmsd.dat
> rms B first :288-328.C,CA,N rmsd.dat
> rms C first :1-88.C,CA,N rmsd.dat

You actually need to use the 'out' keyword before your output file
names (i.e. "out rmsd.dat").

> how should I define *first* for each and every trajectory?

You can use a 'reference' command to explicitly define the first frame
of each trajectory as a reference structure, e.g.:

parm A.prmtop
trajin A.mdcrd parm A.prmtop
reference A.mdcrd 1 parm A.prmtop [A_first]
rms A ref [A_first] :1-88.C,CA,B out rmsd.dat

Hope this helps,


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 Fri Jul 29 2016 - 08:00:02 PDT
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