From: Ryan McGreevy (
Date: Thu Mar 03 2016 - 13:36:28 CST

With such large negative values, my guess is you incorrectly calculated the
ccc with the potential map (the output from mdff griddx that you used in
NAMD) instead of the original density map. The potential is inverted from
the density, giving you the negative numbers. If you recalculate the ccc
with the density, you will likely see similar numbers, but positive,
therefore indicating an improved fit.

On Thu, Mar 3, 2016 at 1:18 PM Bylund, Tatsiana (NIH/NIAID) [F] <> wrote:

> if my ccc goes from -0.8 to -0.88 from start to finish (5'000 frames),
> does it mean that the density map wasn't fitted very well?
> thank you!
> ------------------------------
> *From:* [] on behalf of
> Bylund, Tatsiana (NIH/NIAID) [F]
> *Sent:* Wednesday, March 02, 2016 7:58 PM
> *To:* Ryan McGreevy;
> *Subject:* Re: vmd-l: how to analyze fitting structure into density map
> That it awesome!!!
> I need to be more careful reading options.
> Thank you so much, Ryan!!!!
> From: Ryan McGreevy <>
> Date: Wednesday, March 2, 2016 at 7:51 PM
> To: "Bylund, Tatsiana (NIH/NIAID) [F]" <>, "
>" <>
> Subject: Re: vmd-l: how to analyze fitting structure into density map
> f mdff check. e.g., -frames 0:10:4999 would compute the correlation for
> every 10th frame, starting with the first and ending at the last, but you
> still get a good idea of how the correlation progresses. Also, in the next
> VMD release (1.9.3), mdff check -ccc will be much faster in general.