[AMBER] Energy values from mdout files (excluding solvent molecules)

From: Eduardo R. Almeida <eduardoe.r.a.hotmail.com>
Date: Thu, 23 Apr 2020 13:01:19 +0000

Dear Amber users,

I would like to analyze the energies printed in the mdout files referring only to the solute molecules. On the other words, I would like to build and analyze the graphics of these properties (potential energy, kinetic energy, total energy, temperature, pressure, density, volume, ...) excluding the values referring to the solvents molecules. Would it be possible?

In order to do that, I used the energy calculation performed by the cpptraj where I selected the solute atoms (only including the lipids molecules) in a atom mask for this calculation. Specifically, this calculation has taken a long time (seven days for a lipid bilayer). Therefore, I would like to know if this alternative really calculates these macroscopic properties generated in the mdout files referring only to the solute molecule.

Best regards,


Eduardo R. Almeida
PhD student, Computational chemistry
Núcleo de Estudos em Química Computacional (NEQC)
Universidade Federal de Juiz de Fora (UFJF)

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Received on Thu Apr 23 2020 - 06:30:02 PDT
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