problem with suddenly freezing of one or more atoms in water solution in quickstep NVT simulations
murat... at gmail.com
Fri Jan 28 15:53:45 UTC 2011
Dear cp2k developers and users,
We have been performing now for some time mixed hamiltonian MD simulations
of an organic molecule in water at the DFT/BLYP level of theory, and in some
simulations we noticed some very awkward behavior: that is, sometimes one or
more atoms suddenly completely stop moving.
We have done various tests to understand this problem. We have now even seen
this behavior in a rather standard MD run of 32 water molecules at T=350 K
using the BLYP XC functional and the TZV2P basisset. Although we start from
a restart file was generated in a special manner (using a strange mixed
hamiltonian), this example here is a rather typical simulation which only
uses coordinates and velocities from a restart file.
We have put an example of 1000 MD steps online at:
In the trajectory file the oxygen atoms with index 4 and 61 (start counting
from 1) are not moving (actually the positions fluctuate in the 3rd decimal
in all our examples).
Has anyone seen this problem before? Is this a bug in the code or are we
doing something wrong?
We know that we can "release" the atoms from their apparent fixed positions
by changing input parameters. For example, increasing the planewave cutoff
seems to reduce the number of atoms that typically get stuck in our
simulations. Changing computer platform or cp2k version does not matter.
Any ideas are welcome.
Many thanks in advance,
Computational Chemistry Group
Van 't Hoff Institute for Molecular Sciences
University of Amsterdam
Science Park 904
1098 XH Amsterdam
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