From: Ada Zhan (zyqfrog10_at_msn.com)
Date: Fri Apr 22 2011 - 16:04:52 CDT


It has actually nothing to do with the version of NAMD.

Date: Sat, 23 Apr 2011 02:30:34 +0530
Subject: Re: vmd-l: RE: New NAMD version 2011-03-03 uses
From: ksubbu85_at_gmail.com
To: zyqfrog10_at_msn.com

i want to intall namd

On Sat, Apr 23, 2011 at 12:05 AM, Ada Zhan <zyqfrog10_at_msn.com> wrote:







From: zyqfrog10_at_msn.com
To: vmd-l_at_ks.uiuc.edu
Subject: Re: New NAMD version 2011-03-03 uses
Date: Thu, 21 Apr 2011 19:52:16 -0600









'domain error' still appear after I tried the following things:
1) use equally spaced windows 0.5/-0.5 for forward/backward. (actually I tested the plugin using FEP tutorial sample output files)
2) use my own FEPout files, with increased no. of windows at ends. (FEPlist)

the analysis can only go through 2 or 3 windows till the error massage comes out.
And no graph pop out. (I have grace installed)


Does anyone have an explanation?
Thanks!


Ada

______________________________________


> From: Chris Chipot [chipot_at_ks.uiuc.edu]


> Sent: Thursday, March 17, 2011 6:09 PM


> To: Christian Jorgensen


> Cc: namd-l_at_ks.uiuc.edu


> Subject: Re: namd-l: New NAMD version 2011-03-03 uses


>


> Hi Christian,


>


> parseFEP assumes that the backward fepout file is the mirror image of the


> forward fepout file, i.e. if in your forward file, you ran from λ = 0 to


> 0.2, then


> the backward file should range from λ = 0.2 to 0. It also assumes that your


> increment, δλ, is the same for the forward and backward transformations.


>


> Cheers,


>


> Chris Chipot


>


>


> On 3/17/11 12:58 PM, Christian Jorgensen wrote:


>> Hi all,


>>


>> when using ParseFEP with a fepout file for the forward and the backward run


>> I keep encountering a domain error of the form


>>


>> 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)


>>


>>


>>


>> Does this invalid argument arising when
calculating sqrt($instant_error_gauss) occur because
$instant_error_gauss is taking values<0?


>> I believe it is causing me issues because the ParseFEP log file stops at λ=0.5


>>


>>


>>


>> #=================================================


>> # Free energy perturbation


>> # --------------------------------


>> #forward/backward λ ∆∆A ∆A δε


>> #


>> #-------------------------------------------------


>> forward: 0.0000 0.0000 0.0000 0.0000


>> forward: 0.1000 -0.9392 -0.9392 0.0506


>> forward: 0.2000 -0.8597 -1.7989 0.1287


>> forward: 0.3000 -0.5557 -2.3547 0.1357


>> forward: 0.4000 -0.5542 -2.9089 0.1381


>> forward: 0.5000 -0.4808 -3.3897 0.1421


>>


>>


>> Any input here would be really helpful


>> thanks


>> Christian


>>


>>


>> ______



--
Chris Harrison, Ph.D.
Theoretical and Computational Biophysics Group
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801

char_at_ks.uiuc.edu Voice: 217-244-1733
http://www.ks.uiuc.edu/~char Fax: 217-244-6078