Steered Molecular Dynamics tutorial

From: James Starlight (
Date: Tue Nov 12 2013 - 03:40:44 CST

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,


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