From: Qiang Zhong (zqiang320_at_webmail.hzau.edu.cn)
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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