Hi,
OK, after checking the code the actual problem is that all of the
framework was laid for writing velocity info to netcdf trajectories,
but the code for the write itself isn't there (however writing
velocities in restart/netcdf restarts actually does work). A patch
fixing this will be released soon. Thanks for the report.
-Dan
On Sat, Aug 31, 2013 at 3:44 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> I'm travelling until wed. so I dont have code access until then, but the
> problem is that including velocity info is relatively new and the original
> imaging routines only ever had to deal with coords. I suspect that
> unfortunately this will need a bugfix. I will let you know when I get back.
>
> -Dan
>
>
> On Saturday, August 31, 2013, Eric Berquist wrote:
>>
>> AmberTools 13 up to bugfix 16, and cpptraj v13.15.
>>
>>
>> On Sat, Aug 31, 2013 at 7:14 AM, Daniel Roe <daniel.r.roe.gmail.com>
>> wrote:
>>
>> > Hi,
>> >
>> > What version of cpptraj are you using?
>> >
>> > -Dan
>> >
>> > On Friday, August 30, 2013, Eric Berquist wrote:
>> >
>> > > I need to reimage a trajectory with velocity information in order to
>> > spawn
>> > > QM/MM trajectories from it at various points. However, when I
>> > > autoimage,
>> > > cpptraj explicitly tells me the resulting trajectory doesn't have
>> > velocity
>> > > information. Is there any way of fixing this without going in and
>> > modifying
>> > > the code myself?
>> > >
>> > > The relevant parts of the cpptraj output follow:
>> > >
>> > > INPUT: Reading Input from STDIN
>> > > [trajin 1e1a.04.md_prod_nvt.nc]
>> > > [1e1a.04.md_prod_nvt.nc] contains 25000 frames.
>> > > [autoimage anchor .9045]
>> > > AUTOIMAGE: To box center based on center of mass, anchor mask is
>> > > [.9045]
>> > > [trajout 1e1a.04.md_prod_nvt_imaged.nc]
>> > >
>> > > PARAMETER FILES:
>> > > 0: 1e1a.prmtop, 99260 atoms, 30638 res, box: Trunc. Oct., 30094 mol,
>> > 30063
>> > > solvent, 25000 frames
>> > >
>> > > INPUT TRAJECTORIES:
>> > > 0: [1e1a.04.md_prod_nvt.nc] is a NetCDF AMBER trajectory containing
>> > > velocities, Parm 1e1a.prmtop (Trunc. Oct. box) (reading 25000 of
>> > > 25000)
>> > > Coordinate processing will occur on 25000 frames.
>> > >
>> > > REFERENCE COORDS:
>> > > No frames defined.
>> > >
>> > > OUTPUT TRAJECTORIES:
>> > > [1e1a.04.md_prod_nvt_imaged.nc] is a NetCDF AMBER trajectory, Parm
>> > > 1e1a.prmtop: Writing 25000 frames (1-Last, 1)
>> > >
>> > >
>> > > Eric Berquist
>> > > Lambrecht Group
>> > > University of Pittsburgh
>> > > _______________________________________________
>> > > AMBER mailing list
>> > > AMBER.ambermd.org <javascript:;>
>> > > 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) 585-9119 (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) 585-9119 (Fax)
--
-------------------------
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) 585-9119 (Fax)
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Received on Thu Sep 05 2013 - 11:00:04 PDT
