[gmx-users] Calculating the energy of one molecule in the

：=== >-- > >Message: 2 >Date: Thu, 11 Oct 2007 14:25:35 +0200 >From: "Xavier Periole" <[EMAIL PROTECTED]> >Subject: Re: [gmx-users] Calculating the energy of one molecule in the > multi-molecule system >To: Discussion list for GROMA

Re: [gmx-users] Calculating the energy of one molecule in the multi-molecule system

To get the bonded energy terms of one molecule in your system you have to generate a trajectory file containing this molecule only: trjconv -f full.trr -n molecule.ndx -o molecule.trr and then rerun the simulation using a tpr containing only the topology of your molecule: grompp -f molecule.md

[gmx-users] Calculating the energy of one molecule in the multi-molecule system

Hi, all, I did a simulation on a system which had more than one molecule in it. After the simulation, I want to check the bond/angle/dihedral energy of one molecule in the system. So I set a energy_grp named DNA in the mdp file, and used the command g_energy to calculate the energy on the ener