Hi All.
I try to use different potential models with an Oh symmetry molecule.
I created a topol with nonbond_params, bonds and angles sections, no
include etc.
Initial configuration comes from another program that deals only rigid
bodies,
potential parameters come from literature, tested with other progs.
This flexible model works fine with gromacs (3.3.3 and 3.3.2).
When I change constrains from none to all-angles (shake/0.0001),
according to manual
all bonds and angles are converted to constrains => rigid molecule.
Simulation, run, molecules remain rigid (verified with various tools)
but I get erroneous pressure.
Especially for very low densities (<0.1 g/ml), where intermolecular
interactions are close to zero,
and pressure is almost independent on intermolecular interactions,
the predicted pressure with all-angles is almost half (9.95 instead of
20, 4.96 instead of 10 etc) of the predicted using
the same topol without constrains or the predicted using the same rigid
model
with other programs that deal rigid bodies.
At higher densities still I get lower pressure but this could come from
potential.
Any idea why this ?
D.D.
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