Hello:
in NAMD-CUDA conf file, setting for explicit TIP3 water
## Integrator
timestep 1.0 # 1 fs/step
# rigidBonds all #with H; needed for 2fs/step
# rigidIteractions 100 #shake max iteractions
rigidBonds water
rigidTolerance 0.000001
# useSettle on #faster than shake for water
leads to
FATAL ERROR: UNABLE TO FIND BOND PARAMETERS FOR HX HX (ATOMS 5635 5633)
------------- Processor 0 Exiting: Called CmiAbort ------------
Reason: FATAL ERROR: UNABLE TO FIND BOND PARAMETERS FOR HX HX (ATOMS 5635
5633)
I remember - unfortunately vaguely - that there is an issue related to how
NAMD treats TIP3 water. Commenting out rigidBonds for water, as with
## Integrator
timestep 1.0
# rigidBonds all #with H; needed for 2fs/step
# rigidIteractions 100 #shake max iteractions
# rigidBonds water # if 1fs/step
# rigidTolerance 1e-08
# useSettle on #faster than shake for water
the simulation goes on without errors,. Though, it is much slower than by
treating with CHARMM/NAMD (with flag rigidRonds water) a system of similar
size (200,000 atoms). I suspect that the above solution is affected by flag
errors. I want to stick to ts = 1 fs.
Thanks for advice
francesco pietra
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Received on Tue May 28 2013 - 01:00:02 PDT
