# Re: free energy,energy,entropy calculation for pushing ATP to active site of kinase!

From: Dong Luo (us917_at_yahoo.com)
Date: Thu Jul 19 2007 - 09:15:13 CDT

With a quick browse of the tutorial, my understanding
is that:
the \$T is defined as 0.6 in previous calculation,
which is still in effect.
10 is the total number of pulling trajectory, used for
calculating the average value of work.

Dong

--- Qiang Zhong <zqiang320_at_webmail.hzau.edu.cn> wrote:

> Dear NAMD users:
> I have use SMD to push ATP to active site of
> kinase,I have got a .out file,
> I want to refer paper "Free Energy Calculation from
> Steered Molecular Dynamics
> Simulations Using Jarzynski's Equality" to calculate
> free energy ,energy, entropy
> , just like Fig.3B in that paper. But example code
> "cumulants.tcl" only provide
> free energy calculation, could someone tell me how
> to do it?
>
> I am also puzzled by the code "cumulants.tcl".
>
> foreach l [array names w] {
>
> set e [lindex \$w(\$l) \$i]
> set texp [expr \$texp + exp([expr - \$e / \$T]) ]
>
> "there \$T means temperature? where is it from? "
>
> set t1 [expr \$t1 + \$e]
> set t2 [expr \$t2 + \$e * \$e]
> }
> lappend Fexp [expr - \$T * log([expr \$texp / 10])]
>
> "why is there a constant value 10? what is it
> meaning? "
>
> lappend F1 [expr \$t1 / 10]
> lappend F2 [expr \$t1 / 10 - \$t2 / 10 + \$t1 *
> \$t1 / 100 ]
>
>