Re: [AMBER] MAXPR error in sander sp job

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
<https://pubs.acs.org/doi/10.1021/acs.chemrev.5b00298>.

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
suggest).
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 <https://pubs.acs.org/doi/10.1021/ja107876p>).

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
&cntrl
ntx=1, ntpr=1, ntwx=1,
imin=5,maxcyc=1, !Single-point energy calculation !on each frame ntb=0,
!Non-periodic
cut=9999., !Calculate all !solute-solute interactions

input for periodic system for SP E calculations
&cntrl
ntx=1, ntpr=1, ntwx=1,
imin=5, maxcyc=1, !Single-point energy calculation on each frame
ntb=1, ntp=0, ntc=2, !periodic
cut=9,
/

thank you and best regards.
Vaibhav

On Mon, Feb 22, 2021 at 6:20 PM David A Case <david.case.rutgers.edu> 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
>
>
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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
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