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Message from discussion membrane relax error
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Alex  
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 More options Jun 20 2011, 11:38 am
From: Alex <libra...@gmail.com>
Date: Mon, 20 Jun 2011 08:38:36 -0700 (PDT)
Local: Mon, Jun 20 2011 11:38 am
Subject: membrane relax error
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I am doing the membrane simulation with Desmond these days and I relax
the system before MD. However, the relax steps always wrong, does
anybody have any suggestions?

THX

---------log----------------

Monitoring job: md_jobs

Molecular dynamics
Job launching command:
$SCHRODINGER/utilities/multisim -PROJ /home/albert/md/md/work/md.prj -
DISP append -JOBNAME md_jobs -HOST localhost -maxjob 0 -cpu "1 2 3" -m
md_jobs.msj -c md_jobs.cfg -description "Molecular dynamics"
md_jobs.cms -mode umbrella -o md_jobs-out.cms

Multisim runs in the umbrella mode.
Booting the multisim workflow engine...
           multisim version: 3.8.3.36
            mmshare version: 20109
                    Jobname: md_jobs
                   Username: albert
            Master job host: localhost
                Subjob host: ares ares ares ares ares ares
                     Job ID: ares-0-4dff6790
            multisim script: md_jobs.msj
       Structure input file: md_jobs.cms
            CPUs per subjob: "1 2 3"
             Job start time: Mon Jun 20 17:30:27 2011
           Launch directory: /home/albert/md/md/work
               $SCHRODINGER: /home/albert/install/desmond3

Parsing the multisim script file...

Summary of user stages:
  stage 1 - task
  stage 2 - minimize, Minimization with restraints on solute heavy
atoms
  stage 3 - minimize, Minimization with restraints on solute heavy
atoms
  stage 4 - minimize, Minimization without any restraints
  stage 5 - simulate, Heating from 0 -> $TEMPERATURE K, H2O Barrier
and Gradual restraining
  stage 6 - simulate, NPT equilibration with H2O Barrier with heavy
atoms restrained
  stage 7 - simulate, NPT equilibration of solvent and lipids
  stage 8 - simulate, NPT with protein heavy atoms anealing 10.0 ->
2.0 kal/mol
  stage 9 - simulate, NPT with C_alpha atoms restrained at 5 kcal/mol
  stage 10 - simulate, NPT with C_alpha atoms restrained at 2 kcal/mol
  stage 11 - simulate, NPT, with no restraints
  stage 12 - simulate
(12 stages in total)

Workflow is started now.

Stage 1 - task
stage[1] task: Detecting system type...
stage[1] task:   It seems a mature model system created for regular
molecular dynamics simulations
stage[1] task: Recognizing traits of system...
stage[1] task:   membrane

Stage 1 completed successfully.

Stage 2 - minimize

Launched Job("ares-0-4dff67a8"):
  Launch time: 2011-06-20-17:30:48
  Jobname    : md_jobs_2
  Stage      : 2 (minimize)

Job("ares-0-4dff67a8") was successfully finished.
  Launch time: Mon Jun 20 17:30:48 2011
  Start time : Mon Jun 20 17:30:51 2011
  End time   : Mon Jun 20 17:31:42 2011
  Duration   : 0h 0' 51"
  CPUs       : 6
  CPU time   : 0h 5' 6"
  Exit code  : 0
  Jobname    : md_jobs_2

Launched Job("ares-0-4dff67f3"):
  Launch time: 2011-06-20-17:32:03
  Jobname    : md_jobs_3
  Stage      : 3 (minimize)

  Stage      : 2 (minimize)

Stage 2 completed successfully.

Stage 3 - minimize

Job("ares-0-4dff67f3") was successfully finished.
  Launch time: Mon Jun 20 17:32:03 2011
  Start time : Mon Jun 20 17:32:05 2011
  End time   : Mon Jun 20 17:32:52 2011
  Duration   : 0h 0' 47"
  CPUs       : 6
  CPU time   : 0h 4' 42"
  Exit code  : 0
  Jobname    : md_jobs_3
  Stage      : 3 (minimize)

Stage 3 completed successfully.

Stage 4 - minimize

Launched Job("ares-0-4dff6837"):
  Launch time: 2011-06-20-17:33:11
  Jobname    : md_jobs_4
  Stage      : 4 (minimize)

Job("ares-0-4dff6837") was successfully finished.
  Launch time: Mon Jun 20 17:33:11 2011
  Start time : Mon Jun 20 17:33:14 2011
  End time   : Mon Jun 20 17:34:00 2011
  Duration   : 0h 0' 46"
  CPUs       : 6
  CPU time   : 0h 4' 36"
  Exit code  : 0
  Jobname    : md_jobs_4
  Stage      : 4 (minimize)

Stage 4 completed successfully.

Stage 5 - simulate
Launch failed; no JobId found.
Command:
['/home/albert/install/desmond3/desmond', '-JOBNAME', 'md_jobs_5', '-
USER', 'albert', '-HOST', 'ares ares ares ares ares ares', '-P', '6',
'-c', 'md_jobs_5-in.cfg', '-overwrite', '-in', 'md_jobs_5-in.cms']
Output:
unsupported operand type(s) for /: 'float' and 'str'
Traceback (most recent call last):
  File "/home/albert/install/desmond3/desmond-v30110/bin/Linux-x86_64/
desmond_startup.py", line 939, in main
    launcher.launch(args)
  File "/home/albert/install/desmond3/desmond-v30110/bin/Linux-x86_64/
desmond_startup.py", line 652, in launch
    self._msj2cfg()
  File "/home/albert/install/desmond3/desmond-v30110/bin/Linux-x86_64/
desmond_startup.py", line 488, in _msj2cfg
    self.cfg = config.msj2cfg(self.msj, None, self.cms,
self._getMacroDict())
  File "/home/albert/install/desmond3/mmshare-v20109/lib/Linux-x86_64/
lib/python2.7/site-packages/schrodinger/application/desmond/
config.py", line 2239, in msj2cfg
    __optimize_cfg(          cfg_ref, model )
  File "/home/albert/install/desmond3/mmshare-v20109/lib/Linux-x86_64/
lib/python2.7/site-packages/schrodinger/application/desmond/
config.py", line 2149, in __optimize_cfg
    optimize_key( cfg, model )
  File "/home/albert/install/desmond3/mmshare-v20109/lib/Linux-x86_64/
lib/python2.7/site-packages/schrodinger/application/desmond/
config.py", line 566, in optimize_key
    diffusion           = 807.015 * math.exp( -4.87 / 1.986E-3 /
temp ) - 0.03 * max( 0, temp - 350 )
TypeError: unsupported operand type(s) for /: 'float' and 'str'

  Jobname    : md_jobs_5
  Stage      : 5 (simulate)
  Retries    : 3

Launch failed; no JobId found.
Command:
['/home/albert/install/desmond3/desmond', '-JOBNAME', 'md_jobs_5', '-
USER', 'albert', '-HOST', 'ares ares ares ares ares ares', '-P', '6',
'-c', 'md_jobs_5-in.cfg', '-overwrite', '-in', 'md_jobs_5-in.cms']
Output:
unsupported operand type(s) for /: 'float' and 'str'
Traceback (most recent call last):
  File "/home/albert/install/desmond3/desmond-v30110/bin/Linux-x86_64/
desmond_startup.py", line 939, in main
    launcher.launch(args)
  File "/home/albert/install/desmond3/desmond-v30110/bin/Linux-x86_64/
desmond_startup.py", line 652, in launch
    self._msj2cfg()
  File "/home/albert/install/desmond3/desmond-v30110/bin/Linux-x86_64/
desmond_startup.py", line 488, in _msj2cfg
    self.cfg = config.msj2cfg(self.msj, None, self.cms,
self._getMacroDict())
  File "/home/albert/install/desmond3/mmshare-v20109/lib/Linux-x86_64/
lib/python2.7/site-packages/schrodinger/application/desmond/
config.py", line 2239, in msj2cfg
    __optimize_cfg(          cfg_ref, model )
  File "/home/albert/install/desmond3/mmshare-v20109/lib/Linux-x86_64/
lib/python2.7/site-packages/schrodinger/application/desmond/
config.py", line 2149, in __optimize_cfg
    optimize_key( cfg, model )
  File "/home/albert/install/desmond3/mmshare-v20109/lib/Linux-x86_64/
lib/python2.7/site-packages/schrodinger/application/desmond/
config.py", line 566, in optimize_key
    diffusion           = 807.015 * math.exp( -4.87 / 1.986E-3 /
temp ) - 0.03 * max( 0, temp - 350 )
TypeError: unsupported operand type(s) for /: 'float' and 'str'

  Jobname    : md_jobs_5
  Stage      : 5 (simulate)
  Retries    : 2


 
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