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

[David Mobley]

Florian,

What would be an appropriate set of parameters?

What we're trying to achieve here is to test whether our choice of PME parameters is adequate. To do this, we wanted to increase the PME accuracy to the point where we saw that the energies stopped changing, and then see if our original parameters were in the "energies have stopped changing" regime, or in the "need to change the parameters more to get the energies to stop changing" regime.

Thanks.

On Feb 17, 2010, at 1:02 PM, Florian Dommert wrote:

> Hello,
> 
> On 16.02.2010, at 20:25, 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.
>> 
> 
> How can you be sure, that the PME parameters are more exact ? Of course if you increase your cutoff in real space, the real space part of the electrostatic interaction is getting more accurate. However changing rcut has an influence on the splitting parameter of the Ewald summation. So increasing the cutoff while keeping rtol constant shifts the splitting paramter to a smaller value, that is perhaps not suitable for a precise calculation of the electrostatics. 
> 
> To answer you final questions. The energy will converge if you have an appropriate set of parameters. 
> 
> Cheers,
> 
> Flo
> 
> 
> 
>> 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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> 
> --
> Florian Dommert
> Dipl.-Phys.
> 
> Institute for Computational Physics
> 
> University Stuttgart
> 
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> 70569 Stuttgart
> 
> Phone: +49(0)711/685-6-3613
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> 
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> 
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David Mobley
dmobley at gmail.com
504-383-3662



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