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) (
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!


The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" (in the *body* of the email)