From: Christian Jorgensen (christian.jorgensen_at_merton.ox.ac.uk)
Date: Fri Mar 25 2011 - 09:42:29 CDT
Hi,
yes, I have input the forward and backward out.fepout files
they looks as follows:
FORWARD:
--------------------------------------------------
# STEP Elec vdW dE dE_avg Temp dG
# l l+dl l l+dl E(l+dl)-E(l)
#NEW FEP WINDOW: LAMBDA SET TO 0 LAMBDA2 0.1
FepEnergy: 0 -7642.8934 -7643.1971 881.2135 880.9137 -0.6036 -0.6036 296.6464 -0.6036
FepEnergy: 500 -7273.7007 -7274.0027 612.9069 612.8692 -0.3397 -0.6252 289.7249 -0.6608
FepEnergy: 1000 -7327.7972 -7328.0491 667.6531 667.4697 -0.4353 -0.4924 298.4395 -0.5314
FepEnergy: 1500 -7409.0807 -7409.4268 744.9350 744.4293 -0.8518 -0.5356 296.7072 -0.6198
-------------------------------------------------
BACKWARD
-----------------------------------------------------------
# STEP Elec vdW dE dE_avg Temp dG
# l l+dl l l+dl E(l+dl)-E(l)
#NEW FEP WINDOW: LAMBDA SET TO 1 LAMBDA2 0.9
FepEnergy: 0 -7655.0249 -7652.9024 884.8457 882.1473 -0.5758 -0.5758 288.2716 -0.5758
FepEnergy: 500 -7387.5152 -7382.0985 632.0322 630.2245 3.6090 2.6838 297.8951 1.5411
FepEnergy: 1000 -7469.0699 -7463.2224 673.3060 671.9263 4.4678 3.1130 303.3947 1.9041
FepEnergy: 1500 -7439.7967 -7433.2523 714.4782 713.0188 5.0850 3.4865 299.7999 2.1354
FepEnergy: 2000 -7397.1479 -7391.9088 726.6143 725.2654 3.8902 3.5432 292.3514 2.2847
FepEnergy: 2500 -7505.8158 -7500.4484 747.2242
-------------------------------------------------------------
This is what I understood was the requirement
Christian
________________________________________
From: Chris Chipot [chipot_at_ks.uiuc.edu]
Sent: Friday, March 25, 2011 2:41 PM
To: Christian Jorgensen
Cc: namd-l_at_ks.uiuc.edu
Subject: Re: namd-l: Domain error ParseFEP
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<mailto:chipot_at_ks.uiuc.edu>
Christophe.Chipot_at_edam.uhp-nancy.fr<mailto: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.
_______________________________________________________________________
This archive was generated by hypermail 2.1.6 : Mon Dec 31 2012 - 23:19:59 CST