From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Thu Jun 28 2012 - 06:10:17 CDT
First of all the wrapping of coordinates doesn't effect velocities and
forces if you have used periodic boundary condition. You will also not need
the dcd trajectory to continue a simulation, only the end coordinates of
your previous run.
If you want to continue a simulation with namd, you would just use the final
coor or restart.coor and the corresponding velocities. If you want to
continue with a different md code, you need to know if that code can read
the files that namd produced or how you would need to translate the files.
If the file format is not equal, it's IMHO not a good idea to translate
velocitiy files as there are to many error sources , like units for example.
But it should be easy to just use the final coordinates and start a new
simulation with another md code and create new velocities there.
Pls. describe what you exactly want to do if that answer doesn't help you.
Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im Auftrag
von Namd Namd
Gesendet: Donnerstag, 28. Juni 2012 12:03
Betreff: namd-l: wrap dcd files
I run md simulations for trajectory analysis. Should I wrap the dcd (
coordinates ) , velocity dcd and force dcd files to do trajectory analysis
or to continue md simulations with a different md simulation software ? I
think that coord, velocity and force values will change when I wrap the
system using VMD ? Could you give me the information about this issue ?
Thanks for the help.
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