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

From: Qiang Zhong (
Date: Thu Jul 19 2007 - 06:11:39 CDT

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 ]

Eager to receive your letter!

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