Dear sir,
I have simulated a box of water molecules using netCDF format (using ntwv=-1 in md input file). This generated trajectory files with velocity information embedded into traj file. Each trajectory file contain 200 frames.
I am trying get restart file with velocity information written into the file.
When I tried to use ptraj as below:-
ptraj xx.top << EOF
trajin aaa.traj 1 5
trajout bbb.rst restart
EOF
I get five restart files and when I look into the files the velocities are not written into the files. Normally, the restart file contain two parts. The top part contain x y z coordinates and the bottom part will contain velocities. But the files I generated using above style does not generate restart file with coordinates and velocities information.
When I scan through Amber manual I could not find description that i want.
Is there any way to get velocity and coordinates written into restart files?
Regards
Vijay Manickam Achari
(Phd Student c/o Prof Rauzah Hashim)
Chemistry Department,
University of Malaya,
Malaysia
vjramana.gmail.com
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Received on Wed Jan 16 2013 - 23:00:03 PST
