VMD-L Mailing List

From: surya narayanan chandrasekaran (sonofsunsurya_at_gmail.com)
Date: Thu Jan 17 2019 - 23:07:35 CST

Hi,

Thanks for the suggestion, But both of the solutions didnot work. I had vmd
1.94 previously i removed it and installed 1.93 supposibly the stable
version and loaded the example output files given in the tutorial. the same
error.
I have ubuntu16.04 in my laptop with vmd 1.94 in it. the same error.

I have tried if there is any other problem between vmd and xmgrace, for
example i saved my RMSD using multiplot.agr the plot immediately opened in
xmgrace.

y dont vmd implement multiplot for this job.

On Thu, Jan 17, 2019 at 6:27 PM soroush ziaei <soroush.ziaei7337_at_gmail.com>
wrote:

> Hi,
>
> because of some problems and many features that have been changed in the
> newer version, My suggestion is to work with Ubuntu 16.04 LTS instead of
> 2018 version.
>
> By the way, I have loaded these files a few minutes ago into fep plugin of
> VMD and easily plotted these values with xmgrace. I think your problem is
> related to loading file!
>
> Please load <aqua-forward-on.fepout> & <aqua-backward-on.fepout>.
>
> I hope to done.
>
>
>
> Regards,
>
> soroush
>
>
>
> Sent from Mail <https://go.microsoft.com/fwlink/?LinkId=550986> for
> Windows 10
>
>
>
> *From: *surya narayanan chandrasekaran <sonofsunsurya_at_gmail.com>
> *Sent: *Wednesday, January 16, 2019 4:58 PM
> *To: *vmd-l_at_ks.uiuc.edu
> *Subject: *vmd-l: FEP tutorial plot error
>
>
>
> Hi,
>
>
>
> I was doing alchemical FEP tutorial. After doing the forward and
> backward step i was trying to analyse the .fepout in the vmd plugin and got
> the below error. My computer is Linux based (ubuntu 18) and i have xmgrace
> and gnuplot installed in it.
>
>
>
> option i selected in the plugin:
>
> TEMP:300
>
> GRM-Charlier: 0
>
> disp (on) for unix ststems only
>
> forward and backward .fepout file loaded
>
> BAR-estimator
>
>
>
> Error: missing close-bracket
>
>
> missing close-bracket
> while executing
> "set lambda1 [format "%8.4f" [lindex $::ParseFEP::fwd_lambda $index]
> set lambda2 [format "%8.4f"
> [lindex ..."
> invoked from within
> "if { [file exists [format "file%d.dat" $file_index] ] } {
> set lambda1 [format "%8.4f"
> [lindex $::ParseFEP:..."
> (procedure "::ParseFEP::fepdisp_unix" line 321)
> invoked from within
> "::ParseFEP::fepdisp_unix "
> (procedure "namdparse" line 47)
> invoked from within
> "namdparse"
> (in namespace inscope "::ParseFEP" script line 16)
> invoked from within
> "::namespace inscope ::ParseFEP {
>
> if { [string length $::ParseFEP::fepofile] < 1 } {
> tk_dialog .errmsg {NamdPlot Error} "No ..."
> 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)
>
>
>
>
> --
>
> Warm regards,
>
> Dr. Suryanarayanan C
>
>
>
>
>
>
> 

-- 
Warm regards,
Dr. Suryanarayanan C
DST-Inspire Faculty,
Department of Chemistry,
National Institute of Technology, Trichy, India 620015.
Mobile: +91-8608908117 <089396%2008173>