Hi,
On Fri, May 17, 2013 at 11:05 AM, Sajeewa Pemasinghe
<sajeewasp.gmail.com> wrote:
> vector vectorforall :* :*
This vector is going to be 0.0. You are saying take the vector from
the COM of all atoms to the COM of all atoms. If you want the average
velocity of all atoms in a residue (assuming you are reading in a
velocity trajectory instead of coordinates) you would need something
like this for every residue:
vector res1V center :1
vector res2V center :2
...
I think this will only work with cpptraj since ptraj requires a second
mask for 'corr' vectors. For ptraj you could *maybe* get away with
specifying all atoms for the second mask, but I'm not sure if the
autocorrelation function will be calculated correctly in that case.
Once you have the vectors you can calculate the autocorrelation
function for each vector with 'timecorr'. As always please read the
manual on the related commands carefully so you understand exactly
what they are doing. It may be useful to try your calculations on a
limited number of frames first and see if the results make sense to
you.
-Dan
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-9119 (Fax)
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Received on Fri May 17 2013 - 11:00:03 PDT
