Re: [AMBER] MAXPR error in sander sp job

From: Vaibhav Dixit <>
Date: Mon, 22 Feb 2021 21:00:42 +0530

Dear David,
I'm interested in computing the vertical energy gaps required to estimate
Marcus parameters for two oxidation states involved in an ET process. The
basis for this is equations 11-16 in the chem rev here

Since I needed SP E for each snapshot I chose the input given on page 134
of the manual (and removed the irims=1 keyword).
Maybe this choice of using non-periodic conditions was not correct (please
I was planning to ultimately do the TI but postponed the calculations due
to the complexity of the setup.

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
figure 2 in JACS 2010 <>).

Thus please help me understand if my approach to calculate vertical energy
gaps and Marcus parameters is correct with the periodic system (if it is
not meaningful with the nonperiodic system).

input for non-periodic system for SP E calcualtions
ntx=1, ntpr=1, ntwx=1,
imin=5,maxcyc=1, !Single-point energy calculation !on each frame ntb=0,
cut=9999., !Calculate all !solute-solute interactions

input for periodic system for SP E calculations
  ntx=1, ntpr=1, ntwx=1,
  imin=5, maxcyc=1, !Single-point energy calculation on each frame
  ntb=1, ntp=0, ntc=2, !periodic

Looking forward to your insightful suggestions and expert comments.
thank you and best regards.

On Mon, Feb 22, 2021 at 6:20 PM David A Case <> wrote:

> On Mon, Feb 22, 2021, Vaibhav Dixit wrote:
> >The E-difference between two states (1 and 2) is 21 kcal/mol under
> >non-periodic and 26 kcal/mol under periodic conditions.
> I don't think anyone on the list understands how you are doing the
> non-periodic calculation. Maybe we don't need to know. Your description
> sounds a lot like a standard thermodynamic integration calculation, where
> one computes the average of the energy difference between two (oxidation)
> states.
> Beyond this, you haven't made the goal of the calculation very clear. Are
> you trying to understand what would happen in a really small water droplet
> compared to solution? Why is the non-periodic result of interest?
> ....dac
> _______________________________________________
> 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 - 08:00:02 PST
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