NAMD energy plugin - dielectric constant

From: Ramin Ekhteiari (ramin_ekh_at_yahoo.com)
Date: Mon Jul 07 2014 - 14:59:42 CDT

• Next message: Giacomo Fiorin: "Re: PMF calculations between membrane and nano particle simulations"
• Previous message: sudipta.mml: "(no subject)"
• Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]

Hi,

I'm trying to calculate pair interaction energy between protein and ligand via NAMD energy plugin. In the active site of the protein near the ligand, there are only 2 or three water molecules were placed, so how should I set the dielectric constant, should it be 1 or more ?

I will appreciate for your answers.

Cheers,
Ramin.

• Next message: Giacomo Fiorin: "Re: PMF calculations between membrane and nano particle simulations"
• Previous message: sudipta.mml: "(no subject)"
• Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]

This archive was generated by hypermail 2.1.6 : Wed Dec 31 2014 - 23:22:34 CST