Hi,
On Sun, Mar 13, 2016 at 11:57 AM, Hirdesh Kumar <hirdesh.iitd.gmail.com> wrote:
>
> It would be great if I can visualize four center of masses as a "single"
> molecule in VMD.
You can do this by writing your vector data as a pseudo trajectory via
'vectraj', e.g.
parm myparm.parm7
trajin mytraj.nc
vector V1 center <mask1>
vector V2 center <mask2>
vector V3 center <mask3>
vector V4 center <mask4>
create vector_traj.nc V1 V2 V3 V4 vectraj trajfmt netcdf \
parmout vector_traj.parm7 noorigin
This will create a pseudo trajectory containing your vector data. To
ensure that this script works as-is you should use the GitHub beta
version of cpptraj. If you want to use the AmberTools version of
cpptraj do not include the 'noorigin' keyword since that is not yet
implemented in that version.
Hope this helps,
-Dan
>
> Thanks,
> Hirdesh
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--
-------------------------
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 Sun Mar 13 2016 - 14:00:03 PDT
