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

[XAvier Periole]

Hi,

what is your vdW scheme ? shift/switch/cut-off function ?

On Feb 16, 2010, at 8:25 PM, Gabriel Rocklin 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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