From: Chris Chipot (chipot_at_ks.uiuc.edu)
Date: Tue May 07 2013 - 00:44:08 CDT
Baogen,
first off, get a recent version of ParseFEP (the current one is 1.8).
Second,
check your statistics before blaming the plugin. Under many circumstances,
not enough data has been accrued, or the stratification strategy is
inadequate
for the transformation you are simulating.
Chris Chipot
On 5/7/13 7:10 AM, dbaogen wrote:
> Dear all,
> The ParseFEP 1.5 can not output the value of free energy using
> BAR-estimator. The fepout files of forward and backward includes 40
> windows, respectively. and total 1 ns is run for each window.
> After treating each window of forward and backward, the error occurred
> to carry out BAR-estimator . The error message is as follow:
> divide by zero
> divide by zero
> while executing
> "expr { $deltaA + $::ParseFEP::kT * log ( $length_backward /
> $length_forward ) } "
> (procedure "::ParseFEP::deltaAtoC" line 2)
> invoked from within
> "::ParseFEP::deltaAtoC $deltaA_0 $len_forward $len_backward "
> (procedure "::ParseFEP::bar_estimate" line 94)
> invoked from within
> "::ParseFEP::bar_estimate"
> (procedure "::ParseFEP::namdparse" line 167)
> invoked from within
> "::ParseFEP::namdparse"
> (in namespace inscope "::ParseFEP" script line 22)
> invoked from within
> "::namespace inscope ::ParseFEP {
> ##if {$::ParseFEP::fepbofile != ""} {set ::ParseFEP::sosindex 1 }
> if { [string length $fepofile] < 1 } {
> tk_dial..."
> invoked from within
> ".parseFEP.runbutton invoke"
> ("uplevel" body line 1)
> invoked from within
> "uplevel #0 [list $w invoke]"
> (procedure "tk::ButtonUp" line 22)
> invoked from within
> "tk::ButtonUp .parseFEP.runbutton"
> (command bound to event)
> /Would you like to give me some help? Thanks in advance./
> Duan Baogen
--
_______________________________________________________________________
Chris Chipot, Ph.D.
Theoretical and Computational Biophysics Group
Beckman Institute
University of Illinois at Urbana-Champaign
405 North Mathews Phone: (217) 244-5711
Urbana, Illinois 61801 Fax: (217) 244-6078
E-mail: chipot_at_ks.uiuc.edu
Christophe.Chipot_at_edam.uhp-nancy.fr
Web: http://www.ks.uiuc.edu/~chipot
http://www.edam.uhp-nancy.fr
The light shines in the darkness, and the darkness has not overcome it.
John 1:5.
_______________________________________________________________________
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