From: Giulia (giulia.palermo_at_iit.it)
Date: Tue Oct 23 2012 - 06:58:38 CDT
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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