Hi,
You need to specify the 'velocity' keyword to trajout in order to
include velocity information, e.g.
trajout output.nc velocity
This should work with the latest version of 13 as well as 14 (but I
recommend you switch to 14).
Note that there is a mistake in the manual; section '28.8.3 trajout'
states the keyword as 'novelocity', with the opposite behavior - this
is wrong.
Hope this helps,
-Dan
On Sat, Apr 19, 2014 at 12:01 PM, Eugene Yedvabny
<eyedvabny.berkeley.edu> wrote:
> Hello Amber community,
>
> In the course of my simulation I've created several NetCDF trajectories
> containing both the positions and velocities of the atoms (mdvel=-1).
> Unfortunately, when I try to combine the trajectories into one trajectory,
> trajout strips off the velocities. My cpptraj script is akin to the
> following:
>
> parm protein.prmtop
> trajin round1.mdcrd
> trajin round2.mdcrd
> trajout combined.mdcrd netcdf
>
> I've tried this on both the latest cpptraj 13.22 and the recently released
> cpptraj 14.0. Both recognize that the original mdcrds have velocities, but
> neither one outputs them into the final trajectory. Am I missing a trajout
> directive or is such a feature not supported for when outputting whole
> trajectories?
>
> Thank you,
> Eugene Yedvabny
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--
-------------------------
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) 585-6208 (Fax)
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Received on Sat Apr 19 2014 - 15:30:03 PDT
