[gmx-users] CONSTRAINED SIMULATIONS
chris.neale at utoronto.ca
chris.neale at utoronto.ca
Sun Jan 24 20:00:53 CET 2010
Dear Giuseppe:
This is a pretty good example of how it can be useful to completely
describe what you are doing at first posting. What you mention could
easily be a problem for a couple of reasons:
1. The manual indicates that you may need more than one shake
iteration in this case (or at least it seems possible that this case
is included in what the manual says, although I admit that it is vague):
Constraint forces The distance between the centers of mass of two
groups of atoms can be constrained and the constraint force monitored.
The distance can be in 1, 2, or 3 dimensions. This method uses the
SHAKE algorithm but only needs 1 iteration to be exact if only two
groups are constrained.
2. The manual also says:
constraint forces can only be calculated between groups that are not
connected by constraints to the rest of the system. If a group
contains part of a molecule of which the bondlengths are constrained,
SHAKE or LINCS and the constraint force calculation here will
interfere with each other, making the results unreliable. This means
that for simulations with constraints = all-bonds in the .mdp file
pulling is limited to whole molecules or groups of molecules. In some
cases this limitation can be avoided by using the free energy code,
see sec. 6.3.
Now I know you say angle restraint, not angle constraint, but again
this complicates the issue.
So:
1. remove the angle restraint and see if the constraint force works as
expected
2. if it does, add back the angle restraint while increasing the
number of shake iterations (I have no idea how you could do that).
Chris.
-- original message --
I don't think it is something related to pbc because my solutes are well
inside the simulation box (as I told you before I visualize them via a movie
while the simulation proceeds).
Nor it is something related to the barostat because I saw that warning
and in order to try to see it work I decided to do NVT simulations.
However, the problem persists.
I'm using angle restraints on the "pulled" group in order to preserve its
orientation with respect to the reference group. Could this be the problem?
Cheers,
Giuseppe
Constraint forces The distance between the centers of mass of two
groups of atoms can be
constrained and the constraint force monitored. The distance can be in
1, 2, or 3 dimensions.
This method uses the SHAKE algorithm but only needs 1 iteration to be
exact if only two
groups are constrained.
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