[gmx-users] QM/MM simulations

Iamkaant iamkaant at gmail.com
Fri Apr 25 16:59:12 CEST 2014 

Seems that the latest git master + patch combination works.
Here is what I did (In order to assure that I did everything properly):
1) Get source code and patch
/*git clone https://gerrit.gromacs.org/gromacs*
Cloning into 'gromacs'...
remote: Counting objects: 163705, done
remote: Finding sources: 100% (163705/163705)
remote: Total 163705 (delta 138299), reused 160687 (delta 138299)
Receiving objects: 100% (163705/163705), 91.59 MiB | 766.00 KiB/s, done.
Resolving deltas: 100% (138299/138299), done.
Checking connectivity... done
*cd gromacs
git fetch https://gerrit.gromacs.org/gromacs refs/changes/95/3395/1 && git
checkout FETCH_HEAD*
remote: Counting objects: 11, done
remote: Finding sources: 100% (6/6)
remote: Total 6 (delta 5), reused 6 (delta 5)
Unpacking objects: 100% (6/6), done.
>From https://gerrit.gromacs.org/gromacs
 * branch            refs/changes/95/3395/1 -> FETCH_HEAD
Note: checking out 'FETCH_HEAD'.

You are in 'detached HEAD' state. You can look around, make experimental
changes and commit them, and you can discard any commits you make in this
state without impacting any branches by performing another checkout.

If you want to create a new branch to retain commits you create, you may
do so (now or later) by using -b with the checkout command again. Example:

  git checkout -b new_branch_name

HEAD is now at b335429... Made ORCA compile./

2)cmake
/*mkdir build-cmake
cd build-cmake
cmake .. -DGMX_MPI=ON -DGMX_QMMM_PROGRAM=ORCA
-DCMAKE_INSTALL_PREFIX=/opt/GROMACS-ORCA/ -DGMX_DOUBLE=on
-DFFTW_LIBRARY=/usr/lib64/libfftw3.so.3*/
No errors, QMMM variable is defined in CMakeCache.txt and src/config.h.

3) Using the same .mdp and .ORCAINFO-files as in previous try, just added
"cutoff-scheme = Verlet" and changed defined in topol.top *.itp files for
"gromos43a2.ff/*.itp" (not sure what for, but grompp insisted on that).
/ */opt/GROMACS-ORCA1/bin/grompp_mpi_d -f LT1.mdp -c confin.gro -n index.ndx
-p topol-.top*
GROMACS:    gmx grompp, VERSION 5.1-dev-20140424-b335429 (double precision)

GROMACS is written by:
Emile Apol         Rossen Apostolov   Herman J.C. Berendsen Par Bjelkmar       
Aldert van Buuren  Rudi van Drunen    Anton Feenstra     Sebastian Fritsch  
Gerrit Groenhof    Christoph Junghans Peter Kasson       Carsten Kutzner    
Per Larsson        Justin A. Lemkul   Magnus Lundborg    Pieter Meulenhoff  
Erik Marklund      Teemu Murtola      Szilard Pall       Sander Pronk       
Roland Schulz      Alexey Shvetsov    Michael Shirts     Alfons Sijbers     
Peter Tieleman     Christian Wennberg Maarten Wolf       
and the project leaders:
Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel

Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2014, The GROMACS development team at
Uppsala University, Stockholm University and
the Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.

GROMACS is free software; you can redistribute it and/or modify it
under the terms of the GNU Lesser General Public License
as published by the Free Software Foundation; either version 2.1
of the License, or (at your option) any later version.

GROMACS:      gmx grompp, VERSION 5.1-dev-20140424-b335429 (double
precision)
Executable:   /opt/GROMACS-ORCA1/bin/gmx_mpi_d
Library dir:  /opt/GROMACS-ORCA1/share/gromacs/top
Command line:
  grompp_mpi_d -f LT1.mdp -c confin.gro -n index.ndx -p topol-.top

Ignoring obsolete mdp entry 'title'
Ignoring obsolete mdp entry 'cpp'
Replacing old mdp entry 'nstxtcout' by 'nstxout-compressed'
Replacing old mdp entry 'xtc_grps' by 'compressed-x-grps'
Replacing old mdp entry 'xtc-precision' by 'compressed-x-precision'

Back Off! I just backed up mdout.mdp to ./#mdout.mdp.17#

NOTE 1 [file LT1.mdp]:
  nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
  nstcomm to nstcalcenergy

Setting the LD random seed to 659639382
Generated 380 of the 1326 non-bonded parameter combinations
Excluding 3 bonded neighbours molecule type 'Protein_A'

NOTE 2 [file topol-.top, line 39]:
  System has non-zero total charge: -1.000000
  Total charge should normally be an integer. See
  http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
  for discussion on how close it should be to an integer.
  


Cleaning up constraints and constant bonded interactions with virtual sites
Removing all charge groups because cutoff-scheme=Verlet
Number of degrees of freedom in T-Coupling group rest is 86.00
nr. of CONNBONDS present already: 23
This run will generate roughly 5 Mb of data

There were 2 notes

Back Off! I just backed up topol.tpr to ./#topol.tpr.6#/
/*/opt/GROMACS-ORCA1/bin/mdrun_mpi_d -v*
GROMACS:    gmx mdrun, VERSION 5.1-dev-20140424-b335429 (double precision)

GROMACS is written by:
Emile Apol         Rossen Apostolov   Herman J.C. Berendsen Par Bjelkmar       
Aldert van Buuren  Rudi van Drunen    Anton Feenstra     Sebastian Fritsch  
Gerrit Groenhof    Christoph Junghans Peter Kasson       Carsten Kutzner    
Per Larsson        Justin A. Lemkul   Magnus Lundborg    Pieter Meulenhoff  
Erik Marklund      Teemu Murtola      Szilard Pall       Sander Pronk       
Roland Schulz      Alexey Shvetsov    Michael Shirts     Alfons Sijbers     
Peter Tieleman     Christian Wennberg Maarten Wolf       
and the project leaders:
Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel

Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2014, The GROMACS development team at
Uppsala University, Stockholm University and
the Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.

GROMACS is free software; you can redistribute it and/or modify it
under the terms of the GNU Lesser General Public License
as published by the Free Software Foundation; either version 2.1
of the License, or (at your option) any later version.

GROMACS:      gmx mdrun, VERSION 5.1-dev-20140424-b335429 (double precision)
Executable:   /opt/GROMACS-ORCA1/bin/gmx_mpi_d
Library dir:  /opt/GROMACS-ORCA1/share/gromacs/top
Command line:
  mdrun_mpi_d -v


Back Off! I just backed up md.log to ./#md.log.9#
Reading file topol.tpr, VERSION 5.1-dev-20140424-b335429 (double precision)
Using 1 MPI process
Using 32 OpenMP threads 
QM/MM calculation requested.
Layer 0
nr of QM atoms 24
QMlevel: RHF/3-21G

Setting ORCA path to: /opt/orca_3_0_0_linux_x86-64...
ORCA initialised...


Steepest Descents:
   Tolerance (Fmax)   =  1.00000e+02
   Number of steps    =         1000
Calling '/opt/orca_3_0_0_linux_x86-64/orca topol.inp >> topol.out'/

ORCA is still running. If it is necessary, I can report on the results when
the calculation converges (or provide any additional info), but it seems
that my issue is solved. 
One more question, is there any tutorial on GROMACS-ORCA QM/MM? I haven't
found any.
Thanks for your help.
Sincerely, Andrey.



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