Per Larsson escribió:
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)
Ok, thank you very much. I will try this
Cheers
/Per
Mark
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--
José Carlos Calvo Tudela
Miembro del Departamento de Arquitectura y Tecnología de Computadores
(http://atc.ugr.es)
y del Equipo de Desarrollo Web de la Universidad de Granada
Universidad de Granada (http://www.ugr.es)
Contacto: jcca...@atc.ugr.es
http://atc.ugr.es/~jccalvo
34 958 240588
646 74 25 54
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