AMBER Archive (2008)
Subject: AMBER: Is there any way I can extract the potential energy of the solute with the solvent instead of the total energy in Amber?
From: Zhao, Zhen (zhaozh) (zhaozh_at_ucmail.uc.edu)
I wonder if there is a command in Amber that allows me to extract the potential energy of a solute (for example, an ion) with all the water molecules? Since the total energy in the output file includes the water - water interactions too.
I understand I can do two calculations, with the solute and without the solute and substract the two total energies. But I think that is not a good way since I am substract two large numbers where the errors might be bigger that the difference.
Thanks for your kind help!