Re: [AMBER] calculating MSD by correcting the center-of-mass-motion

From: Vijay Manickam Achari <>
Date: Mon, 13 Jan 2014 08:59:33 +0000 (GMT)

Dear Hannes,

Thanks for the info.


Vijay Manickam Achari
(Phd Student c/o Prof Rauzah Hashim)
Chemistry Department,
University of Malaya,

On Friday, 10 January 2014, 20:02, Hannes Loeffler <> wrote:
On Fri, 10 Jan 2014 11:27:51 +0000
Vijay Manickam Achari <> wrote:

> Dear Sir,
> I have treid to run stfcdiffusion comamnd from cpptraj.
> the command I used is as blow.
> stfcdiffusion mask :BCM.1 out diffusion_in_XY_plane.dat time 5 avout
> distance com xy
> What I wanto calculate is the diffusion of atom number 1 from residue
> BCM.
> I get the output file with 5 columns with the first one representing
> time.
> But I find difficulty in finding the meaning of those columns wiht
> the firstone to the time evolution.
> Could you explain briefly what the coluns aer reperesenting. Further
> I get another file called "distance" with only one line data in it. 
> I want the diffusion along  xy plane.

The output file should contain a header explaining what is in each
column (maybe Dan forgot to include that).  Column 2-4 is for x, y, z
and column 5 is the data for your chosen direction i.e. xy (this column
is actually redundant as you could easily compute this from cols 2 and 3

You get a file named "distance" because you have asked for it with
avout (the next argument to the right is a filename).

"com" requests for the center-of-mass motion of the atoms in "mask"
which seems to be useless here since you obviously want to compute the
MSD for a single atom.  I would also think that the MSD for a single
atom won't be well determined statistically.

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