Re: [AMBER] 3D-RISM options

From: Ryan Pavlovicz <>
Date: Tue, 14 May 2019 17:10:31 -0700

Thanks Tyler. This helps a lot.

When trying to run with --treeDCF, I get the following error:

ERROR: unknown option: '--treeDCF'

I believe I have the most up-to-date version of AmberTools, since I just
downloaded and installed it last week (although I get an 'amber18'
directory when I decompress the download.) Additionally, when I run
update_amber --upgrade, I see that "No major upgrade available".

In your last response, I noticed that you used "treecodeOrderTCF" instead
of the "treeTCFOrder" mentioned in the Manual. So I tried --treecodeDCF as
well, which resulted in the same unknown option error.

Any idea what I'm doing wrong?

Thanks again,


On Tue, May 14, 2019 at 3:44 PM Tyler Luchko (Lists) <> wrote:

> Hi Ryan,
> > On May 14, 2019, at 2:45 PM, Ryan Pavlovicz <> wrote:
> >
> > Hi,
> >
> > I am interested using 3D-RISM for the purpose of predicting hydration
> sites
> > at protein/protein interfaces and would like some help/suggestions on how
> > to optimize both runtime and accuracy.
> >
> Just so you know, the treecode parameters are new and, AFAIK, there
> haven’t been any studies on optimizing the speed of water placement
> calculations. Hydration sites are relatively coarse grained features, so
> high precision (low tolerance) calculations are probably not necessary.
> > I understand that the use of treecode can help speed up the calculation.
> Is
> > the best way to implement this by setting --treeDCF 1 --treeTCF 1
> > --treeCoulumb 1? I see a bunch of other treecode-related flags and
> > suggestions in the Amber19 manual, but I don't quite understand which
> > should be used. Guidance here would be greatly appreciated.
> >
> Yes, these flags will turn on treecode summation, just don’t add the ‘1’
> for rism3d.snglpnt (this is an error in the manual). In addition, you
> should set the MAC and Order for each of DCF, TCF, and Coulomb. The
> values of these depend on the numerical precision you want. Table 7.1 in
> manual gives some suggestions.
> For example, if you are setting the tolerance to 1e-4 then the
> --treecodeOrderTCF should be -2*(3 + log10(1e-4)) = 2. Likewise,
> --treecodeOrderDCF should be 4 and --treecodeOrderCoulomb should be 6.
> Along with the recommended MAC values, this *should* prevent any loss of
> precision due to using treecode but these are not hard and fast rules. If
> you are going to do many calculations, it would be worth your time to try
> some different order values to see if you maintain the precision you want.
> If you are only going to do a few, you might want to play it safe and add 2
> to each parameter; e.g., --treecodeOrderTCF 4.
> > I also understand that additional speed up can be accomplished by
> modifying
> > the grid spacing. For the rism3d.snglpnt calculations, would running with
> > --grdspc 0.5, 0.5, 0.5 --buffer 7 be reasonable for speedup for water
> > placement purposes without sacrificing too much accuracy? What are the
> > default values here?
> >
> The default grid spacing is 0.5 A, which is probably the most commonly
> used for water placement. If you are using Placevent, I believe that it
> always centers waters on a grid site, so the grid spacing will affect the
> placement of discrete waters. Note that a 0.25 A grid spacing will require
> 8X computing time and memory.
> The default for buffer is 14 A. You can experiment with buffer sizes. If
> the interface is buried, I think a 7 A buffer should be fine.
> > Also, is there any known advantage to using SPCE vs TIP3P when it comes
> to
> > native water recovery? And how sensitive would the water placement be
> with
> > different NaCl concentrations? Is the 5 mM NaCl concentration used in
> Dan's
> > tutorial reasonable?
> >
> I don’t know what the effects of ions will be. I would either use pure
> water or the physiological concentration of ions relevant for your
> application. Note that including ions will require more calculation time
> and may require different grid and treecode parameters.
> > Finally, as far as output, I only need the O.dx file for placement of
> water
> > positions with Is there a way to silence the H1, Na+, and
> Cl-
> > output to prevent my disk space issues? Relatedly, is the calculation of
> > these required if I'm only interested in the O distributions?
> There is no way to silence these files and all distributions must be
> computed. Pure water calculations are at least twice as fast.
> Hope this helps,
> Tyler
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Received on Tue May 14 2019 - 17:30:02 PDT
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