Free Energy using atomic coordinates as CVs

From: Teerapong Pirojsirikul (
Date: Thu Jul 11 2013 - 17:59:31 CDT

Dear NAMD users,

I have been working on an RNA system. The catalytic cell of this RNA is the
main region I'm focusing on. There is also an ion bound in this region. I'd
like to search for any other biding sites of this ion. The sampling method
I'm using is the temperature accelerated MD (TAMD), which is integrated
into the main MD integrator via a tcl force script. The ion Cartesian
coordinates (xyz) are chosen as CVs (3 CVs total) and the 3D PMF is to be
constructed as the function of them. I'd like to ask for the idea of how to
treat my system in order to get a meaningful result. Here is what I have
done so far. I have constrained the rotation and translation of the RNA
using the colvar module in NAMD. As stated above, because the catalytic
region is the site of interest, thus, the translation of the RNA is
removed by constraining the distance between a dummy atom and the center of
mass of the catalytic region and the rotation of the active site is
constrained by using the orientation colvar component and a harmonic
restraint. An additional global rotation of the RNA backbone is also
blocked by using the same approach done in the catalytic site. Do you think
this is an appropriate way to treat my system? Any comments are very


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