My two cents, looking back at the original question:
Can Amber TI do uncharged to charged? Yes, it can. The GPU code will do
the same thing the CPU pmemd code will do.
Is this advisable to do, and can one trust the results? That is a whole
different question, and lots of reading is required.
Adrian
On 9/14/17 7:51 AM, David A Case wrote:
> On Wed, Sep 13, 2017, Jason Swails wrote:
>>> Which mutation? A mutation with a change in net charge? I've never tried,
>>> but I THINK the main concern is that the pme reciprocal calculation won't
>>> converge, so in principle you could just have an ion that changes along
>>> with lambda.
>>>
>> PME with a net charge in most programs is no problem -- it applies what's
>> referred to as a "net neutralizing plasma" to ensure the sum converges.
>> The way this is done in practice, I believe, is to simply omit the k=0 term
>> in the reciprocal sum (which is the divergent term in charged cells). This
>> is physically equivalent to taking that net charge and smearing a
>> neutralizing countercharge equally over the mesh.
>>
>> The effect this has on computed thermodynamic properties has been
>> investigated before (with one of the earlier papers being coauthored by Tom
>> Cheatham ...
> I also like the contemporaneous paper from Tom Darden:
>
> %A T. Darden
> %A D. Pearlman
> %A L.G. Pedersen
> %T Ionic charging free energies: Spherical versus periodic boundary
> conditions
> %J J. Chem. Phys.
> %V 109
> %P 10921-10935
> %D 1998
>
> A nice recent overview is here:
>
> %A T. Simonson
> %A B. Roux
> %T Concepts and protocols for electrostatic free energies
> %J Mol. Simul.
> %V 42
> %P 1090-1101
> %D 2016
>
> which (like the Darden paper) presents some detailed numerical examples.
> My take: ion charging energies (i.e. solvation free energies) have
> small relative uncertainties, but association energies can be affected
> by perturbations that change the net charge. These problems can be
> noticeable (on the order of 1 kcal/mol) with boxes of 25 Å or so, and
> should become smaller for larger systems. (But note that a one-sentence
> summary doesn't do justice to either paper!)
>
> ...hope this helps...dac
>
>> Naturally the size of this effect depends heavily on the size of the box,
>> with this effect being far more muted in large unit cells. Keep in mind
>> that most TI calculations are performed using a thermodynamic cycle, so
>> assuming that care is taken when defining this cycle (e.g., the net charge
>> states of the model compound mutation and the mutation in the system of
>> interest are the same with similar solvent environments), then these
>> effects largely cancel when computing the desired free energy.
> This is true, but one has to be careful: sometimes one leg of the cycle
> is for a small model compound, and the other leg is for a protein. In such
> cases, the box sizes might be quite different, which will limit the extent
> of cancellation of error.
>
> ...hope this helps...dac
>
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--
Dr. Adrian E. Roitberg
University of Florida Research Foundation Professor
Department of Chemistry
University of Florida
roitberg.ufl.edu
352-392-6972
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Received on Thu Sep 14 2017 - 06:00:02 PDT
