[gmx-users] energy group exclusions

Hi When we define energy group exclusions e.g. like in manual energygrp excl = Protein Protein SOL SOL and do md rerun, then only non-bonded interactions between Protein and SOL are computed. I am wondering what happens to bonded interactions within the protein, do they contribute to energies even

[gmx-users] energy group exclusions - are forces calculated?

hi, Short question: if I define energy group exclusions between, say, group A and B - will members of group A and B be completely invisible to each other, or is simply their interaction energy not calculated or recorded in the energy output? long version: I'd like to set up a simulation in which

RE: [gmx-users] Energy Group Exclusions

From: Bob Johnson <[EMAIL PROTECTED]> Reply-To: Discussion list for GROMACS users To: GROMACS Mailing List Subject: [gmx-users] Energy Group Exclusions Date: Tue, 16 May 2006 15:08:02 -0400 Hello everyone, I'm simulating a nanotube on a substrate. My substrate is just a simple i

[gmx-users] Energy Group Exclusions

Hello everyone, I'm simulating a nanotube on a substrate. My substrate is just a simple impenetrable wall of closely packed atoms. To restrict the substrate to a planar geometry I am using position restraints on substrate atoms as well as using energy group exclusions (energygrp_exl = substrate sub