From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Jul 18 2012 - 10:36:23 CDT

How about using an empty .vmdrc in case there are other errors
that could be causing problems. You should then be able to run VMD
in text mode, and have it call a simple test script that does a "puts"
and see if you can get at least that much working. Once you get that
working, getting your real script to work should be less trouble.

Cheers,
  John

On Wed, Jul 18, 2012 at 11:31:17AM -0400, Wang Yi wrote:
> Actually, it didn't...
> ___________________________
> Yi (Yves) Wang
> Duke University
> On 2012-7-18, at a:,*aa**11:23, John Stone wrote:
>
> Hi,
> Okay, I see your problem:
>
> Invalid axes location: on
>
> You have errors in your .vmdrc or in the main .vmdrc (if you edited it)
> which are causing the Tcl interpreter to skip subsequent script
> evaluations.
> I think you need to look at your .vmdrc and any other scripts it calls
> and
> fix that problem. Once that is fixed, I would expect your problems to
> go
> away.
>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Wed, Jul 18, 2012 at 11:17:52AM -0400, Wang Yi wrote:
>
> That's a good idea and it helped me find the real problem:
>
> not a single line of the script was executed by vmd.
>
> I made a test script:
>
> puts "Test"
>
> set test_var [expr 1+100]
>
> exit
>
> Also got no output. The program started and exited "normally".
>
> What also appears odd, is that the program finds 16 CPUs always.
> Probably
>
> 8core+hyperthreading. But even after I submit the job as a single
> CPU job,
>
> it still finds 16 CPUs.
>
> ___________________________
>
> Yi (Yves) Wang
>
> Duke University
>
> On 2012-7-18, at a:,*aa**11:04, John Stone wrote:
>
> Hi,
>
> I find it odd that you're not getting any output from the
> namdenergy
>
> plugin in the console at all. If at the end of your script, you
> just
>
> run "namdenergy" with no parameters, I would expect it to print
> out a
>
> bunch of usage information to the console. What happens if you do
> that
>
> on your cluster? Do you get any console output, or does it just
> return
>
> as before?
>
> Cheers,
>
> John Stone
>
> vmd_at_ks.uiuc.edu
>
> On Wed, Jul 18, 2012 at 10:55:37AM -0400, Wang Yi wrote:
>
> Hi John,
>
> Thanks for your reply. Yes we have NAMD on the cluster. I
> invoked
>
> the same
>
> binary executable file that we use to do routine NAMD
> simulations.
>
> And
>
> what's odd is that there's no error message. The namdEnergy
> appears
>
> to be
>
> version 1.3. I will try the latest version next. Here's all it
> gave
>
> me:
>
> Thus no job control in this shell.
>
> ================================================
>
> JOB STARTED ON: Wed Jul 18 10:48:43 EDT 2012
>
> ================================================
>
> Machine: dbchem-n44.dscr.duke.local
>
> Info) VMD for LINUXAMD64, version 1.9 (March 14, 2011)
>
> Info) http://www.ks.uiuc.edu/Research/vmd/
>
>
> Info) Email questions and bug reports to vmd_at_ks.uiuc.edu
>
>
> Info) Please include this reference in published work using
> VMD:
>
> Info) Humphrey, W., Dalke, A. and Schulten, K., `VMD -
> Visual
>
> Info) Molecular Dynamics', J. Molec. Graphics 1996, 14.1,
> 33-38.
>
> Info)
> -------------------------------------------------------------
>
> Info) Multithreading available, 16 CPUs detected.
>
> Info) Free system memory: 30701MB (95%)
>
> Info) No CUDA accelerator devices available.
>
> Info) Dynamically loaded 2 plugins in directory:
>
> Info) /home/dbchem/yw34/lib/vmd/plugins/LINUXAMD64/molfile
>
> Invalid axes location: on
>
> Info) VMD for LINUXAMD64, version 1.9 (March 14, 2011)
>
> Info) Exiting normally.
>
> Here's the command to run VMD:
>
> vmd -dispdev text -e ~/bin/namd_intE.tcl -args
> /home/XXXXX/xxxx.psf
>
> /home/XXXXX/xxxx.dcd /home/XXXXX/par_all36_cgenff.prm
>
> /home/XXXXXX/namd/NAMD_2.8b1_Source_CentOS5/Linux-x86_64-g++/namd2
>
> /netscratch/yw34/namdEng /home/XXXXX/tmp3.eng
>
> All paths are absolute paths. And the same command runs fine
> when I
>
> run it
>
> on the login terminal.
>
> Here's the content of namd_intE.tcl
>
> package require namdenergy
>
> set dcd_file_name [lindex $argv 1]
>
> set psf_file_name [lindex $argv 0]
>
> set par_file_name [lindex $argv 2]
>
> set bin_file_name [lindex $argv 3]
>
> set temp_file_prefix [lindex $argv 4]
>
> set output_file [lindex $argv 5]
>
> puts $argv
>
> mol load psf $psf_file_name dcd $dcd_file_name
>
> set host [atomselect top "resname CB7"]
>
> set guest [atomselect top "resname NC4"]
>
> namdenergy -vdw -elec -sel $host $guest -ofile $output_file
> -par
>
> $par_file_name -exe $bin_file_name -diel 1.0 -switch 16.0
> -cutoff
>
> 18.0
>
> -tempname $temp_file_prefix
>
> exit
>
> Thanks.
>
> ___________________________
>
> Yi (Yves) Wang
>
> Duke University
>
> On 2012-7-18, at a:,*aa**10:46, John Stone wrote:
>
> Hi,
>
> Do you have NAMD installed on your cluster? The namdenergy
>
> plugin
>
> works
>
> by launching NAMD. If NAMD is either unavailable or has
> some
>
> unexpected
>
> problem launching on the cluster, then the namdenergy plugin
> would
>
> not
>
> succeed, however I would normally expect it to emit some
> kind of
>
> warning
>
> or error messages to the VMD console or to the Tk console
> during
>
> the
>
> attempted
>
> run. What output does namdenergy give you when you run it?
>
> Cheers,
>
> John Stone
>
> vmd_at_ks.uiuc.edu
>
> On Tue, Jul 17, 2012 at 11:28:06PM -0400, Wang Yi wrote:
>
> Dear VMD users,
>
> I was trying to use the text mode of VMD to calculate
> complex
>
> interaction
>
> energies from a series of long trajectories. I decided
> to
>
> submit the
>
> job
>
> to the cluster and let it run in batch mode. But I found
> an
>
> interesting
>
> problem -- the "namdenergy" command doesn't run at all
> when I
>
> run
>
> the job
>
> remotely.
>
> First, I did include "package require namdenergy".
>
> Secondly, the same tcl script, runs perfectly when I run
> it on
>
> the
>
> command
>
> line of the login-terminal.
>
> Third, as long as the script is submitted to a remote
> computer
>
> node,
>
> VMD
>
> seems to have skipped namdenergy. No error message,
> program
>
> exited
>
> normally.
>
> Has anyone seen this kind of behavior before?
>
> Thanks.
>
> ___________________________
>
> Yi (Yves) Wang
>
> Duke University
>
> --
>
> NIH Resource 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/ Fax: 217-244-6078
>
> --
>
> NIH Resource 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/ Fax: 217-244-6078
>
> --
> NIH Resource 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/ Fax: 217-244-6078

-- 
NIH Resource 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/       Fax: 217-244-6078