[gmx-developers] PME-Switch vs. PME

[Berk Hess]

Hi,

You don't mention your, critical, cut-off parameters.
I guess you used a long switching range. The switch is only intended to 
avoid
cut-off artifacts (and therefore does not act on the reciprocal).

Any switching function should only be applied over a very short range.
As with PME ewald_rtol is usually 10^-5, you don't really need the switch,
and if you do want to use it, you should switch over 0.05 nm or less.

But in 4.6 you can use exact cut-off's, either with the Verlet cut-off 
scheme,
or at a high cost also with the group cut-off scheme. Thus PME-switch is 
no longer needed
and we should deprecate it in 4.6.

Cheers,

Berk

On 03/06/2013 07:13 PM, Michel Cuendet wrote:
>
> Hi,
>
> I tried to compare PME and PME-switch for a small peptide in solution 
> with Amber96. I was surprised to see that when introducing the Switch 
> function, only the real-space energy is affected, whereas the 
> reciprocal-space part is not. The difference in total energy is huge, 
> about 4919 kJ/mol for my system. Below are the numbers. Shouldn't the 
> reciprocal energy be "switched" as well, in the spirit of what the 
> error function does in Eq. (4.160) and (4.161) of the 4.6.1 manual?
>
> Unfortunately, the energy is not just shifted by a constant. Comparing 
> two different conformations with PME and PME-Switch gives me a 
> DeltaDeltaE of the order of 58 kJ/mol. I also compared the energies 
> with Amber12, and found that PME reproduced the Amber electrostatics 
> within 21 kJ/mol, with a DeltaDeltaE below 2 kJ/mol comparing the two 
> conformations in gromacs and Amber12.
>
> I ran extensive simulations of this peptide with gromacs 4.5.5 and 
> PME-Switch (using various enhanced sampling methods). The peptide 
> would never stay folded, whereas it has been reported to have a 
> significant folded population in simulations with the same force field 
> and cutoffs done with the Amber8 package. Do you think this could be 
> due to the altered electrostatics? I can't see any other explanation 
> at the moment.
>
>
> Gromacs 4.5.5 PME :
> Coulomb-142898.323974
> Coulomb (SR)-221730.3613
> Coul. recip.-24396.81872
> Potential-204582.3431
>
> Gromacs 4.5.5 PME-Switch :
> Coulomb-142898.323974
> Coulomb (SR)-226649.5443difference = -4919.1830
> Coul. recip.-24396.81872
> potential-209501.5261
>
> Gromacs 4.6.1 PME, coulomb-modifier=none
> Coulomb-142898.32373
> Coulomb (SR)-221730.4063
> Coul. recip.-24396.46875
> potential-204592.1719
>
> Gromacs 4.6.1 PME-switch, coulomb-modifier=none
> Coulomb-142898.32373
> Coulomb (SR)-226649.625difference = -4919.2188
> Coul. recip.-24396.46875
> potential-209511.3906
>
>
> I can send files and more elaborate data if required.
>
> Thanks and kind regards,
> Michel
>
>
> ==========================================================
> Michel Cuendet, PhD
> Molecular Modeling Group
> Swiss Institute of Bioinformatics
> CH-1015 Lausanne
> Switzerland
> http://lausanne.isb-sib.ch/~mcuendet/ 
> <http://lausanne.isb-sib.ch/%7Emcuendet/>
> ==========================================================
>
>
>
>
>
>
>
>
>

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