Re: Steered Molecular Dynamics tutorial

From: James Starlight (
Date: Wed Nov 13 2013 - 12:11:57 CST

I'd like to specify some points about steered MD in NAMD.

1) In I should define upperboundaries and lowerboundaries to
prevent movement of my ligand in xy plane if it leaves ligand cavity. As I
understand upperboundaries - lowerboundaries = length of the pore inside my
protein . How I could measure it ?

2) What should I do if the bulk ligand (hydrophobic contacts are the main
stabilized interactions witthin protein interior) haven't pulled from the
protein interior although of big forces been applied to all non-hydrogen
ligand atoms?


2013/11/12 James Starlight <>

> Dear Namd users!
> I have some questions after studing NAMDs steered MD tutorial following
> each of its steps..
> 1) Some methodological issues. It's not clear for me how I could 1)
> obtained list of Ca atoms of my protein (I understood that I should do
> selection in VMD but how save it as the output in txt?) needed for the
> file. Also I dont understand how I could obtain precise values
> for the lowerboundary and upperboundary XY values in based on
> my PDB loaded in the VMD ?). Fnally does it possible to use some script in
> VMD which would automatically shows me sidechains affected ligand motion
> seen in the initial (pull) trajectory (in case of the tutorial it was some
> hydrophobic clusters)?
> Finally I have also theoretical question about linkage of the PMF with the
> free energy value. From the general assumption the barrier regions seen in
> the histograms (where big forces are detected) should correspond to the big
> values of delta G shouldn't it ? It there any general relationships between
> both of that parameter in MD. Does it possible to calculate precise delta G
> value of the studied process (e.g ligand dissociation) based on my SMD
> (assuming that I've simulated the investigated process several times ( in
> several windows) obtaining convergence in each of them)?
> Thanks for help,
> James

This archive was generated by hypermail 2.1.6 : Wed Dec 31 2014 - 23:21:54 CST