Dear all,
I recently encountered a behaviour in pmemd (Amber9), that I do not
understand:
In a protein MD simulation with explicit solvent and periodic boundary
conditions some of the water molecules adopted such distant positions
that a format overflow in the restart file took place. Using ptraj and
the coordinates from the ASCII trajectory file, I imaged all solvent
molecules back into the box; the protein then protruded partly over the
water box boundaries, which I don't consider an issue (but please
correct me, if I am wrong here).
I also copied the velocity information from the original restart file to
the imaged one.
Restarting the pmemd calculation, however, yields "vlimit exceeded for
step" errors printed on STDOUT for the first 4 steps, and then the
program terminates, although the simulation had run without problems before.
When I did an MD simulation with just a single step to obtain the
energies, I found that the energy contributions from bonds, angles,
dihedrals and electrostatics are very similar to those of the original
restart structure, but vdW is five times larger, EPtot halved, and EKtot
almost 10,000 times larger. Obviously, there seems something wrong with
the velocities. However, I ensured that the velocity information in the
imaged restart file is really identical to that of the original one.
Can someone explain this to me? Where is my mistake?
Any hints are welcome.
Thanks in advance,
Anselm Horn
Bioinformatik
Friedrich-Alexander-Universität Erlangen-Nürnberg
Germany
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Received on Wed Apr 23 2008 - 06:07:46 PDT
