Hi,
On Mon, Apr 13, 2015 at 8:05 AM, Jose Borreguero <borreguero.gmail.com> wrote:
> I would like to use cpptraj or ptraj to load a trajectory and then create a
> new trajectory with the center of mass of the residues. I don't see a way
> from reading the manual, but I may be missing something.
What you describe is possible but not easy or straightforward. You
could potentially do a bunch of 'vector center' commands, write them
out as vector pseudo trajectories (in a format that is easily
manipulated like PDB), then manually combine them.
However, if judging from your other recent email you are looking to
calculate the atomic fluctuation of the center of mass it may be
easier (relatively speaking) to perform the atomic fluctuation
calculation on each individual vector pseudo-traj separately and
combine those results, something like:
parm myparm.parm7
trajin mytraj.nc
reference avg.rst7
rms reference
vector v1 center :1 trajout v1.nc trajfmt netcdf parmout vector.parm7
vector v2 center :2 trajout v2.nc trajfmt netcdf
vector v3 center :3 trajout v3.nc trajfmt netcdf
run
clear trajin
parm vector.parm7 [vparm]
trajin v1.nc parm [vparm]
atomicfluct f1 out fluct.agr
run
clear trajin
trajin v2.nc parm [vparm]
atomicfluct f2 out fluct.agr
run
clear trajin
trajin v3.nc parm [vparm]
atomicfluct f3 out fluct.agr
run
A bit complicated but I think it should work. You could also try to
get fancy by giving your vector pseudo-trajectories numerical suffixes
and using the 'ensemble' command with 'nosort' instead of 'trajin' to
get it all done in one shot, e.g.
vector v1 center :1 trajout v.nc.001 trajfmt netcdf parmout vector.parm7
vector v2 center :2 trajout v.nc.002 trajfmt netcdf
vector v3 center :3 trajout v.nc.003 trajfmt netcdf
run
clear trajin
parm vector.parm7 [vparm]
ensemble v.nc.001 nosort parm [vparm]
atomicfluct out fluct.agr
run
Caveat: I *think* the above input will work but I haven't had a chance
to test it so no guarantees. But do let me know if you try it and it
doesn't work or you still have questions.
-Dan
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Mon Apr 13 2015 - 09:30:03 PDT
