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
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Received on Fri Aug 30 2013 - 13:00:02 PDT
