Re: [AMBER] MAXPR error in sander sp job

From: Vaibhav Dixit <>
Date: Tue, 23 Feb 2021 10:20:12 +0530

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
Please do point out if I'm missing/confusing some aspects here.
Thank you and best regards.

On Mon, Feb 22, 2021 at 11:43 PM David A Case <>

> 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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> AMBER mailing list

Dr. Vaibhav A. Dixit,
Visiting Scientist at the Manchester Institute of Biotechnology (MIB), The
University of Manchester, 131 Princess Street, Manchester M1 7DN, UK.
Assistant Professor,
Department of Pharmacy,
Birla Institute of Technology and Sciences Pilani (BITS-Pilani),
VidyaVihar Campus, street number 41, Pilani, Rajasthan 333031.
Phone No. +91 1596 255652, Mob. No. +91-7709129400,
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Received on Mon Feb 22 2021 - 21:00:02 PST
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