module Analyze


Clicked A Few Times
Dear developers!

I am now trying to perform some test concerning molecular dynamics.
I have nwchem-6.5+mpi on my computer. But I don't quite understand if I should run dna example in parallel session, as there is an analyze module (in documentation it is said that this module should not be runned in parallel mode):

md
system dna_em
sd 100
end

task md optimize

task shell "cp dna_em.qrs dna_md.rst"

md
system dna_md
equil 0 data 1000
record scoor 10
isotherm 100.0
record rest 100
end

task md dynamics

analyze
system dna_md
reference dna_em.qrs
file dna_md.trj
super dna_super.trj
rmsd
scan dna_scan
end

task analyze

I have the following output after parallel mode:
   Northwest Computational Chemistry Package (NWChem) 6.5
------------------------------------------------------


                   Environmental Molecular Sciences Laboratory
Pacific Northwest National Laboratory
Richland, WA 99352

                             Copyright (c) 1994-2014
Pacific Northwest National Laboratory
Battelle Memorial Institute

            NWChem is an open-source computational chemistry package
distributed under the terms of the
Educational Community License (ECL) 2.0
A copy of the license is included with this distribution
in the LICENSE.TXT file

                                 ACKNOWLEDGMENT
--------------

           This software and its documentation were developed at the
EMSL at Pacific Northwest National Laboratory, a multiprogram
national laboratory, operated for the U.S. Department of Energy
by Battelle under Contract Number DE-AC05-76RL01830. Support
for this work was provided by the Department of Energy Office
of Biological and Environmental Research, Office of Basic
Energy Sciences, and the Office of Advanced Scientific Computing.


          Job information
---------------

   hostname        = localhost.localdomain
program = nwchem
date = Tue Jan 26 15:23:57 2016

   compiled        = ??_???_27_16:57:07_2015
source = /usr/local/Nwchem-6.5
nwchem branch = 6.5
nwchem revision = 26243
ga revision = 10506
input = dna.nw
prefix = dna.
data base = ./dna.db
status = startup
nproc = 2
time left = -1s



          Memory information
------------------

   heap     =     131066 doubles =      1.0 Mbytes
stack = 4718591 doubles = 36.0 Mbytes
global = 1572864 doubles = 12.0 Mbytes (distinct from heap & stack)
total = 6422521 doubles = 49.0 Mbytes
verify = yes
hardfail = no


          Directory information
---------------------

 0 permanent = .
0 scratch = .




                               NWChem Input Module
-------------------


                                 Prepare Module
--------------

Force field                           amber


Directories used for fragment and segment files

                                      /usr/local/Nwchem-6.5/src/data/amber_s/
/usr/local/Nwchem-6.5/src/data/amber_q/
/usr/local/Nwchem-6.5/src/data/amber_x/
/usr/local/Nwchem-6.5/src/data/amber_u/
./

Parameter files used to resolve force field parameters

                                      /usr/local/Nwchem-6.5/src/data/amber_s/amber.par
/usr/local/Nwchem-6.5/src/data/amber_q/amber.par
/usr/local/Nwchem-6.5/src/data/amber_x/amber.par
/usr/local/Nwchem-6.5/src/data/amber_u/amber.par
./amber.par
PDB geometry dna.pdb

Created segment                       ./DT_5.sgm
Created segment ./DG.sgm
Created segment ./DC.sgm
Created segment ./DA_3.sgm

Created sequence                      ./dna.seq


Parameter file /usr/local/Nwchem-6.5/src/data/amber_s/amber.par
Parameter file /usr/local/Nwchem-6.5/src/data/amber_q/amber.par
Parameter file /usr/local/Nwchem-6.5/src/data/amber_x/amber.par
Parameter file /usr/local/Nwchem-6.5/src/data/amber_u/amber.par

Total charge 0.000000

Created topology                      dna.top

Topology                              dna.top

No command file found: Default restart directives

Solute centered in x-dimension
Solute centered in y-dimension
Solute centered in z-dimension

Boxsize determined to                     1.968800    2.003300    2.599200


Created restart                       dna_em.rst


Task  times  cpu:        0.0s     wall:        0.0s


                               NWChem Input Module
-------------------



Task  times  cpu:        0.4s     wall:        0.4s


                               NWChem Input Module
-------------------



Task  times  cpu:        0.0s     wall:        0.0s


                               NWChem Input Module
-------------------



Task  times  cpu:        3.9s     wall:        3.9s


                               NWChem Input Module
-------------------


                              Analysis Input Module
---------------------


                                 Analysis Module
---------------


Reference coordinates read from dna_em.qrs

Number of atoms is   388
Topology read from dna.top

Opening trj file dna_md.trj
Closing trj file

Trajectory file header from dna_md.trj

Opening trj file dna_md.trj

Opening copy file dna_super.trj



mpirun noticed that process rank 1 with PID 11248 on node localhost.localdomain exited on signal 11 (Segmentation fault).


make: *** [all] error 139

And following output after sequential mode:
             Northwest Computational Chemistry Package (NWChem) 6.5
------------------------------------------------------


                   Environmental Molecular Sciences Laboratory
Pacific Northwest National Laboratory
Richland, WA 99352

                             Copyright (c) 1994-2014
Pacific Northwest National Laboratory
Battelle Memorial Institute

            NWChem is an open-source computational chemistry package
distributed under the terms of the
Educational Community License (ECL) 2.0
A copy of the license is included with this distribution
in the LICENSE.TXT file

                                 ACKNOWLEDGMENT
--------------

           This software and its documentation were developed at the
EMSL at Pacific Northwest National Laboratory, a multiprogram
national laboratory, operated for the U.S. Department of Energy
by Battelle under Contract Number DE-AC05-76RL01830. Support
for this work was provided by the Department of Energy Office
of Biological and Environmental Research, Office of Basic
Energy Sciences, and the Office of Advanced Scientific Computing.


          Job information
---------------

   hostname        = localhost.localdomain
program = nwchem
date = Tue Jan 26 15:45:50 2016

   compiled        = ??_???_27_16:57:07_2015
source = /usr/local/Nwchem-6.5
nwchem branch = 6.5
nwchem revision = 26243
ga revision = 10506
input = dna.nw
prefix = dna.
data base = ./dna.db
status = startup
nproc = 1
time left = -1s



          Memory information
------------------

   heap     =     131066 doubles =      1.0 Mbytes
stack = 4718591 doubles = 36.0 Mbytes
global = 1572864 doubles = 12.0 Mbytes (distinct from heap & stack)
total = 6422521 doubles = 49.0 Mbytes
verify = yes
hardfail = no


          Directory information
---------------------

 0 permanent = .
0 scratch = .




                               NWChem Input Module
-------------------


                                 Prepare Module
--------------

Force field                           amber


Directories used for fragment and segment files

                                      /usr/local/Nwchem-6.5/src/data/amber_s/
/usr/local/Nwchem-6.5/src/data/amber_q/
/usr/local/Nwchem-6.5/src/data/amber_x/
/usr/local/Nwchem-6.5/src/data/amber_u/
./

Parameter files used to resolve force field parameters

                                      /usr/local/Nwchem-6.5/src/data/amber_s/amber.par
/usr/local/Nwchem-6.5/src/data/amber_q/amber.par
/usr/local/Nwchem-6.5/src/data/amber_x/amber.par
/usr/local/Nwchem-6.5/src/data/amber_u/amber.par
./amber.par

Deleted existing topology             dna.top

Deleted existing sequence             ./dna.seq

PDB geometry                          dna.pdb


Created sequence                      ./dna.seq


Parameter file /usr/local/Nwchem-6.5/src/data/amber_s/amber.par
Parameter file /usr/local/Nwchem-6.5/src/data/amber_q/amber.par
Parameter file /usr/local/Nwchem-6.5/src/data/amber_x/amber.par
Parameter file /usr/local/Nwchem-6.5/src/data/amber_u/amber.par

Total charge 0.000000

Created topology                      dna.top


Deleted existing restart              dna_em.rst

Topology                              dna.top

No command file found: Default restart directives

Solute centered in x-dimension
Solute centered in y-dimension
Solute centered in z-dimension

Boxsize determined to                     1.968800    2.003300    2.599200


Created restart                       dna_em.rst


Task  times  cpu:        0.0s     wall:        0.0s


                               NWChem Input Module
-------------------



Task  times  cpu:        0.6s     wall:        0.6s


                               NWChem Input Module
-------------------



Task  times  cpu:        0.0s     wall:        0.0s


                               NWChem Input Module
-------------------



Task  times  cpu:        5.6s     wall:        5.7s


                               NWChem Input Module
-------------------


                              Analysis Input Module
---------------------


                                 Analysis Module
---------------


Reference coordinates read from dna_em.qrs

Number of atoms is   388
Topology read from dna.top

Opening trj file dna_md.trj
Closing trj file

Trajectory file header from dna_md.trj

Opening trj file dna_md.trj

Opening copy file dna_super.trj

make: *** [all] segmentation fault

Besides I have different out-files in these two cases. Can you explain me a reason?

But I need to obtain trajectory file. So what should I do in order to get this information?
And what data would be written in .trj while parallel mode?

Clicked A Few Times
Dear Anastasia,

In addition to the 'reference' and 'file' keywords, you need to specify which frames you want to include in the analysis. Use the 'frames' keyword.
Also, the analysis module does run in parallel.


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