From: Mert Gür (gurmert_at_gmail.com)
Date: Fri Oct 05 2012 - 15:01:03 CDT
Hi JC,
Thanks a lot for your response.
The potential in TMD is
U= 0.5 k/N ( RMS(t)-RMS*(t) )^2
If you take the gradient of it then the force becomes (According to my
derivation),
F= -k/N^2 ( 1-RMS*(t)/RMS(t) ) (R-R_target)
So there is an extra N. Does " k = K/it->second.size()" takes care of that ?
I use the following definition for RMS. Maybe the person who implemented it
used a different definition.
http://en.wikipedia.org/wiki/Root-mean-square_deviation_(bioinformatics)
I am sending you a separate e-mail with my detailed derivation.
Best,
Mert
On Fri, Oct 5, 2012 at 2:26 PM, JC Gumbart <gumbart_at_ks.uiuc.edu> wrote:
> What about this line?
>
> k = K/it->second.size();
>
>
> On Oct 2, 2012, at 12:43 PM, Mert Gür wrote:
>
> Dear all,
>
> I wonder if the equation shown in the following link is correct?
>
> http://www.ks.uiuc.edu/Research/namd/2.7/ug/node41.html
>
> Is it k or k/N. If it is k/N (as written in the link) then there must be a
> second division by N in the source code (
> http://www.ks.uiuc.edu/Research/namd/doxygen/GlobalMasterTMD_8C-source.html)
> which I can not find.
>
> Can anyone comment on this?
>
> Best,
>
> Mert
>
>
>
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