I extracted trajectories with -pbc center -mol to obtain ones with
molecules that form different energy groups in all combinations and then
rerunned the simulation. This procedure was described here
http://lists.gromacs.org/pipermail/gmx-users/2007-October/030104.html
I seem to get a reasonable interaction energy throughout the simulation
and no zeroes. Is this a good procedure to calculate interaction energy?
The reason why I am doing energy calculations posteriori is that a
solvent molecule enters the calixarene cavity but I don't know which one
is doing that until after the simulation.
--- Begin Message ---
On 4/02/2011 1:05 AM, Gordan Horvat wrote:
I'm doing molecule dynamics of a calixarene in a acetonitrile box with
pbc, energy groups defined and npT constant. When I extract
interaction energies with g_energy from edr file I expect them to be
pretty much constant because I see no significant conformational
changes or changes in distance between energy groups and that is true
for one part of simulation when the molecule is completely in the box.
But when a molecule partially leaves the box energies of interaction
for that part which is out of the is box is not calculated (bonded or
with other energy groups) and interaction energy sometimes drops to
0.000 for a period of time even though the distance between groups
doesn't change.
I tried extracting energies through rerunning simulation on
trajectories which were converted with -pbc nojump or -pbc mol -center
but that gave zero energies all the time.
How can I fix this energy calculation problem?
So, having run your original simulation with pre-defined energy groups,
starting from the mdrun output files, what commands reproduce your
observations?
Mark
--- End Message ---
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