Hi Daniel,
You do have some mind-reading abilities, as I do want to calculate the
atomic fluctuations. However, I am going to use the 'vector' command
to output the each residue CM trajectory and then combine them into a
single CRD file, as I want to calculate other quantities besides
fluctuations.
Thanks a lot for your help!
-Jose
On 4/13/15, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> 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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>
--
Jose Borreguero Calvo
Neutron Data Analysis and Visualization Division
Oak Ridge National Laboratory
PO BOX 2008 MS6454
OAK RIDGE TN 37831-6454
Work/Cell: 678-793-6463
work: borreguerojm.ornl.gov , http://neutrons.ornl.gov/ndav,
http://camm.ornl.gov
personal: borreguero.gmail.com , http://www.borreguero.com
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Received on Mon Apr 13 2015 - 10:30:06 PDT
