AW: extract velocities

From: Norman Geist (
Date: Wed Oct 24 2012 - 00:34:56 CDT



if you haven't set "binaryrestart yes", then the vel files will be in PDB
format, what is pretty readable. Otherwise they are bincoor I guess, which
is easy to load and resave with VMD. VMD will threat this files as
coordinates, as the velocities are also saved as X Y Z, and therefore it's
easy to work with vel files in VMD.


But I don't know the unit of the values.


Norman Geist.


Von: [] Im Auftrag
von Giulia
Gesendet: Dienstag, 23. Oktober 2012 13:59
Betreff: namd-l: extract velocities


Dear all,


I have an equilibrated (for c.a. 160 ns) ternary enzyme/DNA/ligand system in
water in the NVT ensemble.

This simulations was done with NAMD. Both the enzyme and DNA were treated
with the last version of the AMBER FF, whereas the ligand was treated with
the gaff FF.

Now, starting from the last equilibrated frame, I would like to use GROMACS.

I will maintain the AMBER topologies, but I need the VELOCITIES of the last
equilibrated point into a readable format (in columns).


Could you please help me in extracting it?

As I know, NAMD saves the velocities into a .vel file. However, I was not
able to extract them in readable format.


Thank you very much

Giulia Palermo

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