From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Dec 03 2013 - 10:46:15 CST

Hi,
  Since the developers of ParseFEP have made many improvements to the
plugin since it was originally released, I would recommend that anyone
encountering issues with the old version immediately try the newest version
which is made available in the VMD 1.9.2 test versions, which can be obtained
by following the steps here:
  http://www.ks.uiuc.edu/Research/vmd/alpha/

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Dec 03, 2013 at 10:08:48AM -0600, Josh Vermaas wrote:
> Hi Shyno,
>
> I've seen this before when I used ParseFEP on simulations that were
> conducted independently (each change in lambda corresponding to its own
> NAMD run, since otherwise it wouldn't get through the queue). ParseFEP is
> very picky about the formatting of the fepout files, especially in VMD
> 1.9, and if each NAMD run is done independently, it doesn't write out some
> of the pieces ParseFEP expects. What I've done is run very short
> simulations (basically the FEP tutorial) where the entire forward and
> backward direction were each one NAMD run to see what the output format
> is, and make sure that I repeat that format when concatenating my
> independent FEPout files together.
>
> Good luck!
> -Josh Vermaas
>
> On 12/02/2013 11:42 AM, Shyno Mathew wrote:
>
> Dear all,
> I am trying to use the parseFEP plugin of VMD version 1.9. FEP
> calculations were done using namd 2.8
> The temperature is set to 300 K, the BAR estimator and disp options are
> turned on. For Gram-Charlier oder, I put 0.
> I am getting the following errors:
> 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)
>
> thanks,
> Shyno
>
> --
> Shyno Mathew
> PhD student
> Department of Chemical Engineering
> Columbia University

-- 
NIH Center for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
http://www.ks.uiuc.edu/Research/vmd/