Re: [AMBER] MAXPR error in sander sp job

From: David A Case <>
Date: Mon, 22 Feb 2021 13:13:13 -0500

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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Received on Mon Feb 22 2021 - 10:30:02 PST
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