From: Chris Chipot (chipot_at_ks.uiuc.edu)
Date: Fri Mar 25 2011 - 09:41:25 CDT
Dear Christian,
parseFEP assumes that it will be fed two files, one for the /forward/ run,
and one for the /backward/ run. Is this the case?
Chris Chipot
On 3/25/11 9:14 AM, Christian Jorgensen wrote:
> Hi all,
> I am performing a bidirectional error analysis where
> I run the forward and backward in a symmetric fashion
> (same starting mutated file A/B)
>
> runFEP 0.0 1.0 0.10 $nSteps ; # 10 windows outward (formally A------>B)
> runFEP 1.0 0.0 -0.10 $nSteps ; # 10 windows outward (formally B----->A)
>
>
>
> However, I keep getting the same error that prevents
> me from carrying out the error analysis:
>
>
>
> domain error: argument not in valid range
> domain error: argument not in valid range
> while executing
> "expr sqrt($instant_error_gauss)"
> (procedure "::ParseFEP::FEP_formula" line 361)
> invoked from within
> "::ParseFEP::FEP_formula $file $file_entropy $file_lambda $window $mean_xi $fororback"
> (procedure "::ParseFEP::normal_parse_log" line 60)
> invoked from within
> "::ParseFEP::normal_parse_log $::ParseFEP::fepofile forward"
> (procedure "::ParseFEP::namdparse" line 172)
> invoked from within
> "::ParseFEP::namdparse"
> (in namespace inscope "::ParseFEP" script line 21)
> invoked from within
> "::namespace inscope ::ParseFEP {
> ##if {$::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)
>
>
>
>
>
>
>
>
> As you can see from the ParseFEP log the process stops after window 7
>
> #=================================================
> # Free energy perturbation
> # --------------------------------
> #forward/backward λ ∆∆A ∆A δε
> #
> #-------------------------------------------------
> forward: 0.0000 0.0000 0.0000 0.0000 WINDOW 1
> forward: 0.1000 -0.5869 -0.5869 0.0575 WINDOW 2
> forward: 0.2000 -0.6208 -1.2077 0.0920 WINDOW 3
> forward: 0.3000 -0.5314 -1.7392 0.1049 WINDOW 4
> forward: 0.4000 -0.5601 -2.2993 0.1250 WINDOW 5
> forward: 0.5000 -0.3727 -2.6720 0.1333 WINDOW 6
> forward: 0.6000 -2.6087 -5.2808 0.1683 WINDOW 7
>
>
>
>
> My question: Has anyone encountered such an error before? Is my procedure correct or not?
>
> Another possibility I have thought of is to do A--------->B
> extract last frame from dcd: B------------A
> however this is not a 'symmetric' procedure in that both processes are run
> as runFEP 0.0 1.0 0.10 $nSteps ; # 10 windows outward
>
>
>
> thanks
> Christian
--
_______________________________________________________________________
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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