Flags for TIP3 water with NAMD/AMBER FF

From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Tue May 28 2013 - 10:46:01 CDT

May I ask about the flags for TIP3 water when using AMBER SB99 under
NAMD2.9-CUDA4.0? The following flags

## 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

give the error
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)

perhaps due to the diferent war TIP3 water is treated by NAMD (freezing
both the O-H bonds and the angle) and AMBER.

Commenting out everything, except ts, the simulation runs correctly albeit
slowly.

## 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

I want to stick to ts = 1 fs.

thanks
francesco pietra

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