• Home

• Overview

• Publications

• Research

• Software

• NAMD

• VMD

• GPU Computing

• Lattice Microbes

• Atomic Resolution Brownian Dynamics

• MDFF

• QwikMD

• VND (Neuronal)

• Other

• Outreach

Building Gramicidin A

Restrain CA Atoms

In this step we create a file for placing harmonic restraints on the CA atoms of our molecule. We keep the restraints on while the system is heated and equilibrated so that the highly variable lipid environment around the protein doesn't disrupt the protein structure too much.

As before, you can color by beta to see which atoms are restrained.

Run this step!     Continue

restrain_ca.vmd

# STEP 8: Restrain CA

# Put harmonic restraints on the CA atoms for heating and unit cell
# equilibration.  Use the coordinates from the last simulation frame.

set all [atomselect top all]
set sel [atomselect top "protein and name CA"]
$all set beta 0
$sel set beta 0.5
$all writepdb restrain_ca.pdb