[gmx-users] QM/MM simulations

[Justin Lemkul]

On 4/25/14, 10:58 AM, Iamkaant wrote:
> 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.

Yes, please report back, regardless of whether the run succeeds or fails.  The 
lack of feedback about the QM/MM interface is one of the reasons various things 
are still broken.  If we don't know about problems, we can't fix them!

> One more question, is there any tutorial on GROMACS-ORCA QM/MM? I haven't
> found any.

If Google doesn't know about it, it doesn't exist.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================