VMD-L Mailing List

From: Wang Yi (dexterwy_at_gmail.com)
Date: Wed Jul 18 2012 - 09:55:37 CDT

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 上午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