Hi,
This is the AMBER mailing list. Perhaps you were looking for the NAMD
mailing list?
http://www.ks.uiuc.edu/Research/namd/mailing_list/
On Tue, May 28, 2013 at 4:43 PM, Francesco Pietra <chiendarret.gmail.com>wrote:
> 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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>
--
Dr. Daniel J. Sindhikara <http://www.dansindhikara.com/Information.html>
Ritsumeikan University <http://www.ritsumei.ac.jp/eng/>
sindhikara.gmail.com <http://www.dansindhikara.com>
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Received on Tue May 28 2013 - 02:30:03 PDT
