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Tutorial 3: Steered molecular dynamics

Steered molecular dynamics (SMD) means external force addition to studied system. This technique allows to steer some process in the direction of interest. For example, it could be applied to study mechanism of protein-ligand association. You could learn more about SMD method on the TCB group page.

This tutorial demonstrates how to push ligand away from active site (dissociation study) or to pull ligand into active site from solvent (association study) by Amber 10. So SMD method will be realized by increasing or decreasing of initial restrained distance between ligand and some active site residue during simulation. Such spherical restraint doesn't specify certain direction so we run SMD with the hope that ligand will find the way by itself. Notice, that when pulling a ligand you must start just near the binding pocket gate to ensure that ligand will enter it. In this example we will use the spring with constant k=150 pN/A that allows 0.5 A thermal fluctuations of the constrained coordinate. Spring length will be changed at constant 5 A/ns velocity.

Here is the smd.in for 1 ns simulation:

Information in the input file:
jar=1  apply SMD
TYPE='DUMPFREQ'  istep1 is the only parameter read, and it sets the frequency at which the coordinates in the distance restraints are dumped to the file specified by the DUMPAVE command in the I/O redirection section
DISANG=dist.RST  the file from which the distance restraint information will be read

And here is the dist.RST for pulling:

Information in the RST file:
iat=125,300  change distance between atoms 125 and 300
r2=10.0  initial distance
rk2=1.0725  k/2 in kcal/mol-A^2
r2a=5.0  final distance

Work of pulling will be written in dist_vs_t file.

By Dmitry Nilov, last modified: 02.11.09