[gmx-users] How to calculate the average distance or energy between two residues?

[Yang Ye]

Hi,

For average distance, you can gather distance v. time by g_mindist, then average them.

For "average energy", you are refering to interaction energy? What you can do is to define two energy groups for two residues separatedly, make a new tpr and use mdrun rerun to get it.
 
Regards,
Yang Ye



----- Original Message ----
From: MoJie Duan <mjduan at smail.hust.edu.cn>
To: gmx-users at gromacs.org
Sent: Sunday, October 7, 2007 10:49:26 PM
Subject: [gmx-users] How to calculate the average distance or energy between two residues?

Hi, everyone!
I want to calculate the average energy (like vdw potential) and average distance between two residues (or two atoms) during a simulation process, how can i do this? Is there any exist package?
best wishes!
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