[gmx-users] Difference between the electrostatic treatments PME/Cut-offs and Reaction Field

[Michael Shirts]

> It should also be noted (and obvious now that I actually look into it) that using dispersion correction results in both the latent heat of vapourisation and density of the alkanes being over estimated (for both Cut-off and Reaction Field, and by the same amount).

That may not be quite the right way to think about it.  The dispersion
correction gives a result that (for homogeneous fluids) is essentially
cutoff independent.  So it's a little "truer" calculation in that it
is relatively independent of your potential cutoff, which is a
nonphysical quantity that's really an artifact of the simulation.

So saying that the properties are overestimated with a dispersion
correction, you're essentially saying that the latent heat of
vaporization and the densities would also be overestimated if your ran
with longer cutoffs, and that they are only right if run with quite
short cutoffs.

On Tue, Jun 4, 2013 at 10:51 PM, Dallas Warren <Dallas.Warren at monash.edu> wrote:
> "Problem" solved.
>
> Just as well I held off reporting the "issue" in full until I had explored everything, I would ended have look a bit stupid ;-)  But asking the initial question helped direct my thinking to the reason.
>
> The issue was the difference in van der Waals cut off between the PME/Cut-off and Reaction Field methods that I was using, 0.9/0.9/0.9 vs 0.8/1.4/1.4  The difference was hidden in the results until you turned off Dispersion Correction, which was what was confusing me and final led to realizing what is going on.  My forehead hurt from slapping it after coming to the realization ...
>
> It should also be noted (and obvious now that I actually look into it) that using dispersion correction results in both the latent heat of vapourisation and density of the alkanes being over estimated (for both Cut-off and Reaction Field, and by the same amount).
>
> Catch ya,
>
> Dr. Dallas Warren
> Drug Discovery Biology
> Monash Institute of Pharmaceutical Sciences, Monash University
> 381 Royal Parade, Parkville VIC 3052
> dallas.warren at monash.edu
> +61 3 9903 9304
> ---------------------------------
> When the only tool you own is a hammer, every problem begins to resemble a nail.
>
>
>> -----Original Message-----
>> From: gmx-users-bounces at gromacs.org [mailto:gmx-users-
>> bounces at gromacs.org] On Behalf Of Mark Abraham
>> Sent: Thursday, 30 May 2013 9:32 PM
>> To: Vitaly Chaban; Discussion list for GROMACS users
>> Subject: Re: [gmx-users] Difference between the electrostatic
>> treatments PME/Cut-offs and Reaction Field
>>
>> Things should be identical - any quantity computed from a zero charge
>> has
>> to be zero :-).
>>
>> Mark
>>
>> On Thu, May 30, 2013 at 1:26 PM, Dr. Vitaly Chaban
>> <vvchaban at gmail.com>wrote:
>>
>> > Hmmm...
>> >
>> > And what does the observed difference look like, numerically?
>> >
>> >
>> >
>> >
>> >
>> > On Thu, May 30, 2013 at 10:14 AM, Mark Abraham
>> <mark.j.abraham at gmail.com
>> > >wrote:
>> >
>> > > No charges = no problem. You can trivially test this yourself with
>> mdrun
>> > > -rerun ;-)  Manual 4.1.4 talks about what RF is doing.
>> > >
>> > > Mark
>> > >
>> > >
>> > > On Thu, May 30, 2013 at 6:38 AM, Dallas Warren
>> <Dallas.Warren at monash.edu
>> > > >wrote:
>> > >
>> > > > In a system that has no charges, should we observe a difference
>> between
>> > > > simulations using PME/Cut-offs or Reaction Field?
>> > > >
>> > > > >From my understanding there should not be, since there are no
>> charges
>> > > > which treatment you use shouldn't' make a difference.
>> > > >
>> > > > However, it does and I am trying to work out why.
>> > > >
>> > > > Any suggestions on the reason?
>> > > >
>> > > > What is it that Reaction Field is doing, does it influence
>> anything
>> > other
>> > > > than long range charge interactions?
>> > > >
>> > > > Catch ya,
>> > > >
>> > > > Dr. Dallas Warren
>> > > > Drug Discovery Biology
>> > > > Monash Institute of Pharmaceutical Sciences, Monash University
>> > > > 381 Royal Parade, Parkville VIC 3052
>> > > > dallas.warren at monash.edu
>> > > > +61 3 9903 9304
>> > > > ---------------------------------
>> > > > When the only tool you own is a hammer, every problem begins to
>> > resemble
>> > > a
>> > > > nail.
>> > > > --
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