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From: Matthew Guberman-Pfeffer <matthew.guberman-pfeffer.uconn.edu>

Date: Mon, 27 Sep 2021 18:42:19 -0400

Dear Amber Community,

I want to compute the change in the (electrostatic) interaction energy between a redox cofactor and the surrounding environment upon a change in redox state. I’ve done this calculation two ways (described below), and I’m wondering if you can please help me understand why the results differ. I need to decide if one way should be preferred over the other.

1) Usng the LIE feature in cpptraj, I give the redox center as mask1 and everything else as mask2, and process the trajectories with topologies corresponding to the two different charge states.

2) Using esander in cpptraj, I compute the electrostatic energy of the entire system for each redox state. I then use the energy function in cpptraj to compute the self-energy of the cofactor in each redox state, and I subtract that energy from the electrostatic energy given by esander to get the interaction energy.

I’d greatly appreciate any thoughts on the pros and cons of these two approaches to compute the change in interaction energy.

Best,

Matthew

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Received on Mon Sep 27 2021 - 16:00:02 PDT

Date: Mon, 27 Sep 2021 18:42:19 -0400

Dear Amber Community,

I want to compute the change in the (electrostatic) interaction energy between a redox cofactor and the surrounding environment upon a change in redox state. I’ve done this calculation two ways (described below), and I’m wondering if you can please help me understand why the results differ. I need to decide if one way should be preferred over the other.

1) Usng the LIE feature in cpptraj, I give the redox center as mask1 and everything else as mask2, and process the trajectories with topologies corresponding to the two different charge states.

2) Using esander in cpptraj, I compute the electrostatic energy of the entire system for each redox state. I then use the energy function in cpptraj to compute the self-energy of the cofactor in each redox state, and I subtract that energy from the electrostatic energy given by esander to get the interaction energy.

I’d greatly appreciate any thoughts on the pros and cons of these two approaches to compute the change in interaction energy.

Best,

Matthew

_______________________________________________

AMBER mailing list

AMBER.ambermd.org

http://lists.ambermd.org/mailman/listinfo/amber

Received on Mon Sep 27 2021 - 16:00:02 PDT

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