On Fri, 10 Jan 2014 11:27:51 +0000
Vijay Manickam Achari <vjrajamany.yahoo.com> 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
obviously).
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.
Cheers,
Hannes.
--
Scanned by iCritical.
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Jan 10 2014 - 04:30:02 PST
