Hi,
The Amber14 manual is up-to-date - the 'novelocity' entry for Amber
NetCDF should have been changed to 'velocity' and its description
updated to 'include velocity information if present'. The 'novelocity'
keyword for Amber Restart and NetCDF restart still function as
advertised.
My apologies for the confusion.
-Dan
On Sat, Apr 19, 2014 at 4:43 PM, Eugene Yedvabny <eyedvabny.berkeley.edu> wrote:
> Thank you Dr. Roe. I saw the 'novelocity' directive and your release notes
> for cpptraj 13 bugfix 22, but it seemed like velocity output only applied
> to restart files.
>
> Are there any man pages or READMEs that list up-to-date commands which have
> not yet trickled into the manual?
>
> Thank you,
> Eugene Yedvabny
>
>
> On Sat, Apr 19, 2014 at 2:59 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
>
>> 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
>> > _______________________________________________
>> > AMBER mailing list
>> > AMBER.ambermd.org
>> > http://lists.ambermd.org/mailman/listinfo/amber
>>
>>
>>
>> --
>> -------------------------
>> 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)
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
--
-------------------------
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 - 16:30:07 PDT
