Philip Shushkov wrote:
Dear GMX-USERS,
I would like to ask you for some advice because I have serious problem
in setting up a PR MD in GROMACS of DPPC monolayer. Prior to actual MD
simulation I have done exhaustive energy minimization up to 10 kJ/mol*nm
convergence criterion. Firstly, I minimized the system with restraints
applied to the heavy atoms of the lipid molecules and then the whole
system consisting of 81 DPPC molecules and 5575 water molecules.
Afterward, in order to avoid some unexpected behavior I minimized the
system with less stringent restraints on the heavy lipid atom which I
would keep in the course of the equilibration, a final step before the
equilibrating MD run. However, though the three stage minimization
procedure which surely relaxed all bad contacts, the first step of the
MD integration gave high positive energy due to the position restraints
contribution. Some trial and error steps allowed me to find that the
problem was in the grompp program and may be the parallelization of
GROMACS. The position restraints were OK with *.tpr file constructed
without the -shuffle option of grompp. Unfortunately, now the LINCS
algorithm crashes and obviously the systems tends to explode. But if I
again turn off the restraints and prepare the *.tpr with -shuffle using
the same starting configuration as before, everything looks very well.
In conclusion, I would like to humbly ask you where the problem could be
and are there any problems reported concerning PR constraint molecular
dynamics in parallel mode in GROMACS.
Position restraints and analytical constraints on the same atoms are
likely to lead to numerical problems, particularly if your initial
structure (to which you are presumably restraining) doesn't satisfy the
constraints (which get re-inforced every integration step).
You can eliminate the parallel code as a source of problems by doing a
test run on one processor.
Mark
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