VMD-L Mailing List

From: Shyno Mathew (sm3334_at_columbia.edu)
Date: Wed Dec 04 2013 - 10:41:18 CST

Hello John and Josh,
Thanks so much for the replies.
John: Like you said, I am trying to download the VMD 1.9.2 test version. Is
there a windows compatible version?
I don't want to update the linux system with new VMD yet, so I was trying
to download test version to my pc.
thanks,
Shyno

On Tue, Dec 3, 2013 at 11:46 AM, John Stone <johns_at_ks.uiuc.edu> wrote:

> 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/
> 

-- 
Shyno Mathew
PhD student
Department of Chemical Engineering
Columbia University