Hi George:
I was aware of your cited guideline, which let me doing the job in the
past. Now I wanted to ask what is wrong about the following flags for
NAMD/SB99
## 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
which 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)
Commenting out everything, except ts, the simulation runs correctly albei
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 was unable to improve on the flags through your guideline.
thanks
francesco
On Tue, May 28, 2013 at 5:21 PM, George Giambasu <giambasu.gmail.com> wrote:
>
> Francesco - I haven't followed the discussion in detail, but you might be
> able to find more on how to use amber ff with namd here:
>
> http://ambermd.org/namd/namd_amber.html
>
> Let me know if that's answering your questions,
>
> gg
>
>
>
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Received on Tue May 28 2013 - 09:00:03 PDT
