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)
Date: Sat Sep 20 2008 - 15:01:59 CDT

Hi, all

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!

Sincerely

Zhen
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