VMD-L Mailing List

From: Shyno Mathew (sm3334_at_columbia.edu)
Date: Mon Dec 09 2013 - 12:23:29 CST

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