23 feb 2009 kl. 12.55 skrev Mark Abraham:
José Carlos Calvo Tudela wrote:
can I use the GROMACS software to get the energy of a protein
conformation?
Yes, but your question is not well-formed. Only energy differences
can have meaning.
Up to now I am using TINKER library (analyze program). Is there any
similar software in GROMACS?
I don't know.
If I'm not mistaken, the energy you get from analyse.x program in
Tinker is the potential energy for a protein in is current
conformation, given a particular force-field.
In that case, you might be able to get the same from Gromacs if you do
a simulation with 0 steps, ie without any integration, and then look
at the potential energy terms in the log file (or do many steps, and
look at the energy before the first step)
Cheers
/Per
Mark
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