positive total energy

From: C. Navarro (kdefuego_at_gmail.com)
Date: Tue Aug 10 2010 - 08:48:59 CDT

Hello all,

I'm having some trouble trying to understand if it can be OK to have
positive energy for a protein during molecular dynamics with namd. I'm
afraid my phisics and termodinamics skills are not enough to answer this
question by myself, so I'm putting it to this list.

After 1 ns dynamics of a cytosolic protein (in water), I have taken the
dcd file and opened in vmd, then calculated the intramolecular energy of
the protein for every frame, with this tcl commands:

set sel [atomselect top "protein"]
package require namdenergy
namdenergy -all -sel $sel -ofile protein-energy.dat

Giving me positive total energies. It is important to say that this is
happening only with one copy of three? of my protein of study, (The
other two proteins show negative energy values); so it is hard to me to
think in an error during the dynamics protocol. By the way, the total
energy of the system (taking all the atoms for the energy evaluation),
still gives negative values (which is fine).

Please, any input to this issue would be very appreciated.


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