Re: Free Energy using atomic coordinates as CVs

From: Jérôme Hénin (
Date: Fri Jul 12 2013 - 05:12:23 CDT

Hi Tee,

> Do you think this is an appropriate way to treat my system?
Do you think this is an appropriate way to treat us?

I'm joking, but really the question is too broad for this list. It's the kind of question one would expect you to ask your advisor. If I answer that, I want to be last author on your paper.
Seriously though: precise, technical questions are much more likely to get answers here.


----- Original Message -----
> 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 welcome.
> Tee

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