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

From: Eduardo R. Almeida <eduardoe.r.a.hotmail.com>
Date: Tue, 21 Apr 2020 03:57:48 +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 tried to use the energy calculation performed by the cpptraj where I could defined a mask of atoms for this calculation. This way, I defined only the residues of the solute. However, this calculation has taken a long time (seven days for a lipid bilayer). I would like to know if this alternative calculate the energies components referring only to the solute molecule.

Best regards,


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Received on Mon Apr 20 2020 - 21:00:02 PDT
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