VMD-L Mailing List

From: Shyno Mathew (sm3334_at_columbia.edu)
Date: Mon Dec 09 2013 - 11:01:38 CST

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