From: Geist, Norman (norman.geist_at_uni-greifswald.de)
Date: Tue May 31 2022 - 01:29:34 CDT
Hey there, I've reported this before for a beta of NAMD-2.13 and the
problem is still present in 2.14:
It seems something is generally going wrong with
"ReplicaUniformPatchGrid". I’ve observed this with my own variant of
H-REMD where I used CheckpointStore and CheckpointLoad to swap the
coordinates between the Hamiltonians. This runs ok for the first
“job” but the restart files that are written in-between (as in
original REMD) using "output"
are broken as they contain overlapping water molecules. Not only that,
even the coordinates in the DCD files contain very close contacts of
below 1A for water-water and protein-water contacts.
I’ve worked around it using just “output” and “reinitatoms”
for coordinate swapping, but the in-memory solution with global
checkpoints would of course be the cleaner solution, as accessive use
of the output command often overwhelms parallel filesystems such as
lustre or beegeefs.
For clarity, it was only a dihedral scaling H-REMD, so a scaling of
VDW interactions is not the reason for the overlapping waters, which
rather seem to be a problem with collecting the patches that are
probably mixed between replicas.
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