Re: [AMBER] Can (cp)ptraj calculate the diffusion of the center of mass?

From: Daniel Roe <>
Date: Thu, 4 Sep 2014 20:17:34 -0600


Check out the 'stfcdiffusion' command in cpptraj (specifically the
'com' keyword), which is an alternative to the traditional 'diffusion'
command with several advanced features. Let me know if you have any
more questions.


On Thu, Sep 4, 2014 at 4:59 PM, Jose Borreguero <> wrote:
> Dear AMBER users,
> I want to calculate the diffusion MSD(t) for the center of mass of atoms
> specified by a mask. The option 'average' in the action command 'diffusion'
> does a different calculation, which is average the atomic MSD(t). I need to
> first average the atomic positions (the center of mass), and then calculate
> its diffusion. Is it possible with ptraj or cpptraj?
> Thanks in advance,
> Jose Borreguero
> _______________________________________________
> AMBER mailing list

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 Thu Sep 04 2014 - 19:30:02 PDT
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