[gmx-users] Dyn. Load Balance changes Cut off

[Johnny Lu]

I see. Thank you.

On Fri, Nov 7, 2014 at 1:38 PM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> Hi,
>
> This is normal. See
>
> http://www.gromacs.org/Documentation/Acceleration_and_parallelization#Hybrid.2fheterogeneous_acceleration
> and manual 3.17.5. The quality of the approximation to full electrostatics
> is the thing that should be conserved, not the cut-off. In the bad old
> days, the cut-off was the only parameter available, but this is not true
> with PME.
>
> Mark
>
> On Fri, Nov 7, 2014 at 7:21 PM, Johnny Lu <johnny.lu128 at gmail.com> wrote:
>
> > Hi.
> >
> > When I read the log file, I see:
> >
> >  PP/PME load balancing changed the cut-off and PME settings:
> >            particle-particle                    PME
> >             rcoulomb  rlist            grid      spacing   1/beta
> >    initial  1.000 nm  1.090 nm      64 64 64 0.117 nm  0.320 nm
> >    final    1.302 nm  1.392 nm      48  48  48   0.156 nm  0.417 nm
> >  cost-ratio           2.08             0.42
> >  (note that these numbers concern only part of the total PP and PME load)
> >
> > So, the cut off that I typed in the mdp file was changed.
> >
> > Will that affect the result of the simulation? I'm using gromacs 4.6.7.
> > Or any cut off will be fine, as long as I use a cut off that is long
> > enough?
> >
> > The force field paper for Amber99SB-ILDN used 1.0 nm for both VdW and PME
> > electrostatic cut off.
> >
> > Thanks again.
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