VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Dec 10 2013 - 10:32:07 CST

Hi,
  Thanks for reporting this and the subsequent followup. I think that
there's a simple change that can be made to the ParseFEP plugin to
make this scenario less confusing. I will send a note to the authors and
suggest a small change that will help in cases like yours where
ImageMagick isn't (yet) installed on the machine, or isn't in the users
path.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Mon, Dec 09, 2013 at 01:23:29PM -0500, Shyno Mathew wrote:
> Dear all,
> was able to fix the error, thanks to Christopher MacDermaid!! the error
> was due to the fact that I didn't have Imagemagick.
> So from these plots, I can get the answer for the previous question:
> So to make the plots of P(deltaU) for the forward and reverse FEP for the
> first strata (lambda =0 to lambda=0.05),
> I should use files: file1.dat.hist and file1.dat.rev.hist
>
> thanks,
> Shyno
>
> On Mon, Dec 9, 2013 at 12:01 PM, Shyno Mathew <sm3334_at_columbia.edu> wrote:
>
> Dear all,
> As mentioned in the previous message, I am getting errors with ParseFEP
> plugin of the VMD test version, VMD 1.9.2a35. The plugin is not
> generating the plots of P(deltaU) for the forward and reverse FEP for
> each strata.
> I am trying to see if I can make these plots to see if FEP has
> converged.
> 1. In my case I have 38 strata
> dlambda= 0.05 for all cases except between 0.50 and 0.60 where
> dlambda=0.005
> So to make the plots of P(deltaU) for the forward and reverse FEP for
> the first strata (lambda =0 to lambda=0.05),
> should I use files: file1.dat.hist and file1.dat.rev.hist
> or should I use files: file1.dat.hist and file38.dat.rev.hist
>
> I am also attaching a file which shows the error while using parseFEP.
>
> Any help will be appreciated,
>
> thanks,
> Shyno
>
> On Sun, Dec 8, 2013 at 11:40 PM, Shyno Mathew <sm3334_at_columbia.edu>
> wrote:
>
> Hi John,
> I installed the test version VMD 1.9.2a35 and was able to run the
> parseFEP plugin. However, I am getting errors shown in the attached
> file.
> I got .png file which shows the deltaG for forward and reverse FEP for
> each strata. But I can't see the plots for probability distributions
> for each strata.
> Initially I thought the error was due to the NVIDIA driver software,
> but it's not the case. I tried the VMD test version on my pc (dual
> boot fedora 19, windows7) and also on the lab machine (fedora 16).
> The same error occurs in both the machines!
> Even though I wrote a script to calculate probability distribution of
> deltaU for each strata, it will be useful to see the output of
> parseFEP plugin.
>
> thanks,
> Shyno
>
> On Wed, Dec 4, 2013 at 11:41 AM, Shyno Mathew <sm3334_at_columbia.edu>
> wrote:
>
> 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
>
> --
> Shyno Mathew
> PhD student
> Department of Chemical Engineering
> Columbia University
>
> --
> Shyno Mathew
> PhD student
> Department of Chemical Engineering
> Columbia University
>
> --
> 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/