From: Brian Radak (bradak_at_anl.gov)
Date: Wed May 31 2017 - 08:33:47 CDT
That does seem a bit unusual. You probably don't need the "splitPatch"
command, since that is default. Exclude 1-2 is also unusual, but makes
perfect sense in this case (the more usual exclude 1-4 should also have
the same effect).
I've also had trouble with small water boxes since the system is so
small - I unfortunately do not have a guaranteed solutions other than to
use the CPU code (as opposed to CUDA, etc).
HTH,
Brian
On 05/31/2017 04:04 AM, M. Wong wrote:
> Dear NAMD users,
>
> I tried to run a simulation of 256 water molecules inside a periodic
> box. I used the parameter and coordinate files generated using AMBER.
> However, I got the following error:
>
> FATAL ERROR: splitPatch hydrogen is required for rigidBonds
>
> Can anyone tell me how to prevent the error from happening?
> The following is my config file:
>
> amber on
> parmfile 256w.top
> ambercoor 256w.crd
>
> set temperature 300
> set outputname eq_256w
>
> firsttimestep 0
> temperature $temperature
>
> # Force-Field Parameters
> exclude 1-2
> cutoff 9.85
> switching off
>
> # Integrator Parameters
> timestep 1.0
> rigidBonds all
> stepspercycle 10
> splitPatch hydrogen
>
> # Constant Temperature Control
> langevin on
> langevinDamping 1
> langevinTemp $temperature
> langevinHydrogen off
>
> # Periodic Boundary Conditions
> cellBasisVector1 19.71 0.0 0.0
> cellBasisVector2 0.0 19.71 0.0
> cellBasisVector3 0.0 0.0 19.71
> cellOrigin 9.855 9.855 9.855
>
> wrapAll on
>
> # PME (for full-system periodic electrostatics)
> PME yes
> PMEGridSpacing 1.0
>
> langevinPiston off
>
> # Output
> outputName $outputname
>
> restartfreq 500
> dcdfreq 500
> outputEnergies 500
>
> minimize 1000
> reinitvels $temperature
>
> run 100000
>
> Your help will be kindly appreciated.
>
> Thanks in advance,
> Marco
-- Brian Radak Postdoctoral Appointee Leadership Computing Facility Argonne National Laboratory 9700 South Cass Avenue, Bldg. 240 Argonne, IL 60439-4854 (630) 252-8643 brian.radak_at_anl.gov
This archive was generated by hypermail 2.1.6 : Mon Dec 31 2018 - 23:20:20 CST