Dear David,
I'm following a very similar/identical procedure for estimating the energy
gaps. The non-periodic nature of the system was the only mistake I was
making, which is corrected now.
Although the TI calculation would do free energy on the fly, one would have
to manually extract SP E (from mdout) to estimate the reorganization
energies. Also, the TI is available for only the CPU version in Amber18,
(but I believe now possible with GPU in Amber20, I will try that soon).
I will surely read the paper carefully to increase my understanding of the
topic.
Please do point out if I'm missing/confusing some aspects here.
Thank you and best regards.
Vaibhav
On Mon, Feb 22, 2021 at 11:43 PM David A Case <david.case.rutgers.edu>
wrote:
> On Mon, Feb 22, 2021, Vaibhav Dixit wrote:
>
> >I'm interested in computing the vertical energy gaps required to estimate
> >Marcus parameters for two oxidation states involved in an ET process.
>
> There doesn't seem to need to be any need to think about non-periodic
> simulations here. Copy the (periodic) prmtop file for one oxidation state
> ("A"), and change the charges to match oxidation state "B" (parmed makes
> this easy to do).
>
> Then (probably using imin=5) take snapshots from the simulation of state
> "A", and get the single point energy using prmtop "A"; repeat with the same
> snapshot, but now use prmtop "B". At each time point, subtract the two.
> Do this for many snaphots and take the average of the difference.
>
> >I was planning to ultimately do the TI but postponed the calculations due
> >to the complexity of the setup.
>
> The TI setup does the above calculation on the fly during a simulation: at
> each point, it computes the "energy gap", the energy difference between the
> two oxidation states. So, it's simpler to do this (in my view) than what
> you are doing. For a clear discussion of how these calculations relate to
> Marcus theory, see this paper:
>
> %A T. Simonson
> %T Gaussian fluctuations and linear response in an electron transfer
> protein
> %J Proc. Natl. Acad. Sci. USA
> %V 99
> %P 6544-6549
> %D 2002
>
> >
> >The purpose of using different box size was to assess the influence of
> this
> >factor on calculated vertical energy gaps and Marcus parameters (since
> >these are known to converge as the system size is gradually increased
>
> Again, if you are in a condensed phase, stick with periodic simulations.
> You can make the unit cell size bigger and bigger to see what kind of
> convergence you are getting.
>
> ...hope this helps...dac
>
>
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>
--
Regards,
Dr. Vaibhav A. Dixit,
Visiting Scientist at the Manchester Institute of Biotechnology (MIB), The
University of Manchester, 131 Princess Street, Manchester M1 7DN, UK.
AND
Assistant Professor,
Department of Pharmacy,
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Birla Institute of Technology and Sciences Pilani (BITS-Pilani),
VidyaVihar Campus, street number 41, Pilani, Rajasthan 333031.
India.
Phone No. +91 1596 255652, Mob. No. +91-7709129400,
Email: vaibhav.dixit.pilani.bits-pilani.ac.in, vaibhavadixit.gmail.com
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Received on Mon Feb 22 2021 - 21:00:02 PST
