VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Jul 18 2012 - 10:04:01 CDT

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