[gmx-users] Position Restraints MD

Philip Shushkov philip.shushkov at gmail.com
Mon Jan 28 10:54:10 CET 2008


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.


University of Sofia
Faculty of Chemistry
Department of Physical Chemistry
Quantum and Computational Chemistry Lab
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