VMD-L Mailing List

From: Shyno Mathew (sm3334_at_columbia.edu)
Date: Sun Dec 08 2013 - 22:40:58 CST

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