Re: [AMBER] 3D-RISM options

From: Tyler Luchko (Lists) <"Tyler>
Date: Tue, 14 May 2019 17:17:38 -0700

Try running

rism3d.snglpnt -h

You should see the full list of options. If you don’t see ‘—treeDCF’ as an option then it is not the current version.


> On May 14, 2019, at 5:10 PM, Ryan Pavlovicz <> wrote:
> 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,
> ryan
> 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
>> _______________________________________________
>> AMBER mailing list
> _______________________________________________
> AMBER mailing list

AMBER mailing list
Received on Tue May 14 2019 - 17:30:02 PDT
Custom Search