VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Jul 18 2012 - 10:47:17 CDT

Hi,
  I'm not sure why you would have trouble with any of those,
perhaps there's an invisible control character mixed in there somewhere.
Try adding the lines back in a couple at a time until you figure out which
one(s) caused the problem.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Jul 18, 2012 at 11:43:36AM -0400, Wang Yi wrote:
> It worked after I emptied the .vmdrc file! Thanks!
> Here's the content:
> menu main on
> menu graphics on
> menu files on
> stage location off
> menu main move 5 650
> menu display move 0 0
> menu graphics move 250 39
> menu files move 120 120
> display projection orthographic
> display resize 750 800
> What could be causing trouble?
> ___________________________
> Yi (Yves) Wang
> Duke University
>
> On 2012-7-18, at a:,*aa**11:36, John Stone wrote:
>
> 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 

-- 
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