[gmx-developers] Gromacs 3.3.4 PME energies keep changing with longer cutoffs

[Ilya Chorny]

It looks like the STD between .7 - 1.1 is large and then it is small beyond
that.  So I would argue that your data suggests that 1.2+ the values are not
changing.

Can the PE fluctuations be do to precision error? Do you keep enough
precision in you trajectory file? Does double precision make the
fluctuations go away.

Cheers,

Ilya


On Tue, Feb 16, 2010 at 11:25 AM, Gabriel Rocklin
<gabriel.rocklin at ucsf.edu>wrote:

> Hi all,
>
> I'm seeing some confusing behavior with Gromacs 3.3.4 and PME
> electrostatics.  My potential energies seem to not to converge a single
> "correct" value as I make the PME parameters more and more exact.
>
> I took 10 snapshots from a single precision, constant volume simulation I'm
> doing of a protein in water and saved them as .gro files with -ndec = 8.  I
> then used mdrun -rerun to re-evaluate their energies using a number of
> different PME parameters.  I found that the energies were not sensitive to
> ewald_rtol or fourierspacing (below certain values), but they were very
> sensitive to rlist and rcoulomb even out to very long distances.
>
> For example, using pme_order=6, spacing=0.1, and tolerance=0.00000001, as I
> increase rlist and rcoulomb together from 0.7 to 2.5nm, I get these
> potential energies for my 10 snapshots:
>
> 0.7 -656927.375 -657225.4375 -656475.0 -656451.875 -657604.8125
> -656090.6875 -657553.25 -657241.8125 -657747.9375 -656863.5625
> 0.9 -654605.375 -654916.1875 -654163.9375 -654132.125 -655300.875
> -653771.5 -655239.875 -654936.875 -655420.75 -654539.25
> 1.0 -654553.5625 -654862.0625 -654108.9375 -654078.0 -655246.875
> -653718.4375 -655182.6875 -654884.3125 -655365.8125 -654486.375
> 1.1 -654536.875 -654842.5 -654094.3125 -654061.25 -655227.9375
> -653701.4375 -655166.5 -654864.3125 -655349.625 -654468.75
> 1.2 -654533.5625 -654842.625 -654087.1875 -654054.5 -655224.625
> -653695.125 -655164.25 -654863.5625 -655340.5 -654463.125
> 1.3 -654531.9375 -654837.0625 -654087.5625 -654054.5625 -655223.6875
> -653694.125 -655161.6875 -654857.5 -655345.0625 -654462.5
> 1.5 -654532.375 -654839.8125 -654086.1875 -654057.25 -655223.25
> -653693.3125 -655164.4375 -654864.1875 -655340.1875 -654461.5625
> 1.8 -654527.125 -654840.3125 -654086.9375 -654054.0625 -655221.25
> -653696.6875 -655155.75 -654860.0625 -655343.5 -654465.8125
> 2.0 -654532.5625 -654843.125 -654083.75 -654053.6875 -655223.375
> -653695.375 -655158.8125 -654860.1875 -655342.3125 -654464.4375
> 2.5 -654535.875 -654838.75 -654089.875 -654055.0625 -655220.25 -653692.75
> -655163.4375 -654857.375 -655337.125 -654461.375
>
> So not only do the numbers keep changing, but the relative energies change
> as well, so that for example going from 2.0 to 2.5 nm, the standard
> deviation of the change in energy across the 10 snapshots is 4 kJ.
>
> The system is a dodecahedral box with a volume of about 500 nm^3.
>
> Is this normal behavior?  Should these values converge to specific
> energies?  And how far out would you normally have to set rcoulomb/rlist to
> see this?
>
> Thanks,
> Gabriel
>
> Gabriel Rocklin
> UCSF Shoichet/Dill Labs
>
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-- 
Ilya Chorny Ph.D.
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