Installation of gromacs-2021.1-qmmm

Hello everyone,
I am Sudarshan Behera, a graduate student, trying to install gromacs-2021.1-qmmm (Files · 2021.1-qmmm · Dmitry Morozov / CP2KInterface · GitLab) for quite a long time now. I could install it but whenever I run “grompp” module I get the following error (I provide proper path to the gromacs executable).

"Unknown left-hand ‘qmmm-active’ in parameter file"

Below are the steps I’ve followed to install it. Please have a look if there are any mistakes.

(I) CP2K installation:
(a) ./install_cp2k_toolchain.sh --enable-cuda=no --with-sirius=no --with-openblas=install
(b) cp /pfs/home/bala/Sudarshan/softwares/cp2k/cp2k-8.1/tools/toolchain/install/arch/* /pfs/home/bala/Sudarshan/softwares/cp2k/cp2k-8.1/arch
source /pfs/home/bala/Sudarshan/softwares/cp2k/cp2k-8.1/tools/toolchain/install/setup
cd /pfs/home/bala/Sudarshan/softwares/cp2k/cp2k-8.1/
make -j 24 ARCH=local VERSION=“psmp” libcp2k

     After this I get a "libcp2k.a" file in the /pfs/home/bala/Sudarshan/softwares/cp2k/cp2k-8.1/lib/local/psmp/ directory.

(II) Gromacs Installation:
(a) downloaded gromacs from Files · 2021.1-qmmm · Dmitry Morozov / CP2KInterface · GitLab
(b) cd /pfs/home/bala/Sudarshan/softwares/gromacs/
mkdir build
cd build
(c) /pfs/home/bala/Sudarshan/softwares/cp2k/cp2k-8.1/tools/toolchain/install/cmake-3.18.5/bin/cmake … -DGMX_INSTALL_NBLIB_API=OFF -DBUILD_SHARED_LIBS=OFF -DGMXAPI=OFF -DGMX_DOUBLE=ON -DGMX_FFT_LIBRARY=fftw3 -DCMAKE_CXX_FLAGS="-I/pfs/home/bala/Sudarshan/softwares/cp2k/cp2k-8.1/src/start" -DGMX_BLAS_USER="/pfs/home/bala/Sudarshan/softwares/cp2k/cp2k-8.1/tools/toolchain/install/openblas-0.3.10/lib/libopenblas.a" -DGMX_LAPACK_USER="/pfs/home/bala/Sudarshan/softwares/cp2k/cp2k-8.1/tools/toolchain/install/openblas-0.3.10/lib/libopenblas.a" -DCMAKE_CXX_STANDARD_LIBRARIES=" -Wl,–allow-multiple-definition -pthread -L/pfs/softwares/admin/sw/target/prl/openmpi/openmpi-2.1.2_gcc-7.2.0/lib -L/pfs/home/bala/Sudarshan/softwares/cp2k/cp2k-8.1/tools/toolchain/install/openblas-0.3.10/lib -L/pfs/home/bala/Sudarshan/softwares/cp2k/cp2k-8.1/tools/toolchain/install/fftw-3.3.8/lib -L/pfs/home/bala/Sudarshan/softwares/cp2k/cp2k-8.1/tools/toolchain/install/libint-v2.6.0-cp2k-lmax-5/lib -L/pfs/home/bala/Sudarshan/softwares/cp2k/cp2k-8.1/tools/toolchain/install/libxc-4.3.4/lib -L/pfs/home/bala/Sudarshan/softwares/cp2k/cp2k-8.1/tools/toolchain/install/libxsmm-1.16.1/lib -L/pfs/home/bala/Sudarshan/softwares/cp2k/cp2k-8.1/tools/toolchain/install/scalapack-2.1.0/lib -L/pfs/home/bala/Sudarshan/softwares/cp2k/cp2k-8.1/lib/local/psmp/exts/dbcsr -L/pfs/home/bala/Sudarshan/softwares/cp2k/cp2k-8.1/lib/local/psmp -L/pfs/home/bala/Sudarshan/softwares/cp2k/cp2k-8.1/tools/toolchain/install/elpa-2020.05.001/lib -L/pfs/home/bala/Sudarshan/softwares/cp2k/cp2k-8.1/tools/toolchain/install/spglib-1.16.0/lib -L/pfs/home/bala/Sudarshan/softwares/cp2k/cp2k-8.1/tools/toolchain/install/cosma-2.2.0/lib -L/pfs/home/bala/Sudarshan/softwares/cp2k/cp2k-8.1/tools/toolchain/install/libvori-201229/lib -lcp2k -ldbcsr -lsymspg -lelpa_openmp -lcosma_pxgemm -lcosma -lgrid2grid -lscalapack -lxsmmf -lxsmm -ldl -lpthread -lxcf03 -lxc -lint2 -lfftw3_mpi -lfftw3 -lfftw3_omp -lmpi -lopenblas -lvori -lstdc++ -lstdc++ -lgfortran" -DGMX_MPI=on -DCMAKE_INSTALL_PREFIX=/pfs/home/bala/Sudarshan/softwares/gromacs/
(d) make -j 24
make install -j 24

Then I find a “gmx_mpi_d” executable in the /pfs/home/bala/Sudarshan/softwares/gromacs/bin/ directory which I guessed would have QMMM capabilities. I execute the following command
/pfs/home/bala/Sudarshan/softwares/gromacs/bin/gmx_mpi_d grompp -f em-qmmm2.mdp -c …/EM/em.gro -p …/topol.top -n …/QM.ndx -o em-qmmm2.tpr
and get the following warnings,
WARNING 1 [file em-qmmm2.mdp, line 27]:
Unknown left-hand ‘qmmm-active’ in parameter file
WARNING 2 [file em-qmmm2.mdp, line 27]:
Unknown left-hand ‘qmmm-qmgroup’ in parameter file
WARNING 3 [file em-qmmm2.mdp, line 27]:
Unknown left-hand ‘qmmm-qmmethod’ in parameter file
WARNING 4 [file em-qmmm2.mdp, line 27]:
Unknown left-hand ‘qmmm-qmcharge’ in parameter file
WARNING 5 [file em-qmmm2.mdp, line 27]:
Unknown left-hand ‘qmmm-qmmultiplicity’ in parameter file

   which I think are because of incapabilities of the gmx_mpi_d executable to read QMMM specific CP2K parameters (keywords). 

Please help me to find out if there are any mistakes while installing the packages or anywhere else. I am also pasting the content the cp2k arch file named “local.psmp” below for reference.

Content of /pfs/home/bala/Sudarshan/softwares/cp2k/cp2k-8.1/arch/local.psmp:

CC = /pfs/softwares/admin/sw/target/cmpl/gcc/gcc-7.2.0/bin/gcc
CXX = /pfs/softwares/admin/sw/target/cmpl/gcc/gcc-7.2.0/bin/g++
AR = ar -r
FC = mpif90
LD = mpif90

DFLAGS = -D__LIBXSMM -D__parallel -D__FFTW3 -D__LIBINT -D__LIBXC -D__SCALAPACK -D__COSMA -D__ELPA -D__SPGLIB -D__LIBVORI

WFLAGS = -Werror=aliasing -Werror=ampersand -Werror=c-binding-type -Werror=intrinsic-shadow -Werror=intrinsics-std -Werror=line-truncation -Werror=tabs -Werror=target-lifetime -Werror=underflow -Werror=unused-but-set-variable -Werror=unused-variable -Werror=unused-dummy-argument -Werror=conversion -Werror=zerotrip -Wno-maybe-uninitialized -Wuninitialized -Wuse-without-only

FCDEBFLAGS = -fbacktrace -ffree-form -fimplicit-none -std=f2008
CFLAGS = -march=native -mtune=native -fno-omit-frame-pointer -g -O3 -funroll-loops $(PROFOPT) -fopenmp -I/pfs/softwares/admin/sw/target/prl/openmpi/openmpi-2.1.2_gcc-7.2.0/include -pthread -I’/pfs/home/bala/Sudarshan/softwares/cp2k/cp2k-8.1/tools/toolchain/install/openblas-0.3.10/include’ -I’/pfs/home/bala/Sudarshan/softwares/cp2k/cp2k-8.1/tools/toolchain/install/fftw-3.3.8/include’ -I’/pfs/home/bala/Sudarshan/softwares/cp2k/cp2k-8.1/tools/toolchain/install/libint-v2.6.0-cp2k-lmax-5/include’ -I’/pfs/home/bala/Sudarshan/softwares/cp2k/cp2k-8.1/tools/toolchain/install/libxc-4.3.4/include’ -I’/pfs/home/bala/Sudarshan/softwares/cp2k/cp2k-8.1/tools/toolchain/install/libxsmm-1.16.1/include’ -I’/pfs/home/bala/Sudarshan/softwares/cp2k/cp2k-8.1/tools/toolchain/install/cosma-2.2.0/include’ -I’/pfs/home/bala/Sudarshan/softwares/cp2k/cp2k-8.1/tools/toolchain/install/elpa-2020.05.001/include/elpa_openmp-2020.05.001/modules’ -I’/pfs/home/bala/Sudarshan/softwares/cp2k/cp2k-8.1/tools/toolchain/install/elpa-2020.05.001/include/elpa_openmp-2020.05.001/elpa’ -I/pfs/home/bala/Sudarshan/softwares/cp2k/cp2k-8.1/tools/toolchain/install/spglib-1.16.0/include -std=c99 -Wall -Wextra -Werror $(DFLAGS)
FCFLAGS = -march=native -mtune=native -fno-omit-frame-pointer -g -O3 -funroll-loops $(PROFOPT) -fopenmp -I/pfs/softwares/admin/sw/target/prl/openmpi/openmpi-2.1.2_gcc-7.2.0/include -pthread -I’/pfs/home/bala/Sudarshan/softwares/cp2k/cp2k-8.1/tools/toolchain/install/openblas-0.3.10/include’ -I’/pfs/home/bala/Sudarshan/softwares/cp2k/cp2k-8.1/tools/toolchain/install/fftw-3.3.8/include’ -I’/pfs/home/bala/Sudarshan/softwares/cp2k/cp2k-8.1/tools/toolchain/install/libint-v2.6.0-cp2k-lmax-5/include’ -I’/pfs/home/bala/Sudarshan/softwares/cp2k/cp2k-8.1/tools/toolchain/install/libxc-4.3.4/include’ -I’/pfs/home/bala/Sudarshan/softwares/cp2k/cp2k-8.1/tools/toolchain/install/libxsmm-1.16.1/include’ -I’/pfs/home/bala/Sudarshan/softwares/cp2k/cp2k-8.1/tools/toolchain/install/cosma-2.2.0/include’ -I’/pfs/home/bala/Sudarshan/softwares/cp2k/cp2k-8.1/tools/toolchain/install/elpa-2020.05.001/include/elpa_openmp-2020.05.001/modules’ -I’/pfs/home/bala/Sudarshan/softwares/cp2k/cp2k-8.1/tools/toolchain/install/elpa-2020.05.001/include/elpa_openmp-2020.05.001/elpa’ -I/pfs/home/bala/Sudarshan/softwares/cp2k/cp2k-8.1/tools/toolchain/install/spglib-1.16.0/include $(FCDEBFLAGS) $(WFLAGS) $(DFLAGS)

LDFLAGS = $(FCFLAGS) -Wl,–enable-new-dtags -pthread -L/usr/lib64 -Wl,-rpath -Wl,/usr/lib64 -Wl,-rpath -Wl,/pfs/softwares/admin/sw/target/prl/openmpi/openmpi-2.1.2_gcc-7.2.0/lib -Wl,–enable-new-dtags -L/pfs/softwares/admin/sw/target/prl/openmpi/openmpi-2.1.2_gcc-7.2.0/lib -L’/pfs/home/bala/Sudarshan/softwares/cp2k/cp2k-8.1/tools/toolchain/install/openblas-0.3.10/lib’ -Wl,-rpath=’/pfs/home/bala/Sudarshan/softwares/cp2k/cp2k-8.1/tools/toolchain/install/openblas-0.3.10/lib’ -L’/pfs/home/bala/Sudarshan/softwares/cp2k/cp2k-8.1/tools/toolchain/install/fftw-3.3.8/lib’ -Wl,-rpath=’/pfs/home/bala/Sudarshan/softwares/cp2k/cp2k-8.1/tools/toolchain/install/fftw-3.3.8/lib’ -L’/pfs/home/bala/Sudarshan/softwares/cp2k/cp2k-8.1/tools/toolchain/install/libint-v2.6.0-cp2k-lmax-5/lib’ -L’/pfs/home/bala/Sudarshan/softwares/cp2k/cp2k-8.1/tools/toolchain/install/libxc-4.3.4/lib’ -Wl,-rpath=’/pfs/home/bala/Sudarshan/softwares/cp2k/cp2k-8.1/tools/toolchain/install/libxc-4.3.4/lib’ -L’/pfs/home/bala/Sudarshan/softwares/cp2k/cp2k-8.1/tools/toolchain/install/libxsmm-1.16.1/lib’ -Wl,-rpath=’/pfs/home/bala/Sudarshan/softwares/cp2k/cp2k-8.1/tools/toolchain/install/libxsmm-1.16.1/lib’ -L’/pfs/home/bala/Sudarshan/softwares/cp2k/cp2k-8.1/tools/toolchain/install/scalapack-2.1.0/lib’ -Wl,-rpath=’/pfs/home/bala/Sudarshan/softwares/cp2k/cp2k-8.1/tools/toolchain/install/scalapack-2.1.0/lib’ -L’/pfs/home/bala/Sudarshan/softwares/cp2k/cp2k-8.1/tools/toolchain/install/cosma-2.2.0/lib’ -Wl,-rpath=’/pfs/home/bala/Sudarshan/softwares/cp2k/cp2k-8.1/tools/toolchain/install/cosma-2.2.0/lib’ -L’/pfs/home/bala/Sudarshan/softwares/cp2k/cp2k-8.1/tools/toolchain/install/elpa-2020.05.001/lib’ -Wl,-rpath=’/pfs/home/bala/Sudarshan/softwares/cp2k/cp2k-8.1/tools/toolchain/install/elpa-2020.05.001/lib’ -L’/pfs/home/bala/Sudarshan/softwares/cp2k/cp2k-8.1/tools/toolchain/install/spglib-1.16.0/lib’ -Wl,-rpath=’/pfs/home/bala/Sudarshan/softwares/cp2k/cp2k-8.1/tools/toolchain/install/spglib-1.16.0/lib’ -L’/pfs/home/bala/Sudarshan/softwares/cp2k/cp2k-8.1/tools/toolchain/install/libvori-201229/lib’ -Wl,-rpath=’/pfs/home/bala/Sudarshan/softwares/cp2k/cp2k-8.1/tools/toolchain/install/libvori-201229/lib’
LIBS = -lsymspg -lelpa_openmp -lcosma_pxgemm -lcosma -lgrid2grid -lscalapack -lxsmmf -lxsmm -ldl -lpthread -lxcf03 -lxc -lint2 -lfftw3_mpi -lfftw3 -lfftw3_omp -lmpi -lopenblas -lvori -lstdc++ -lstdc++

FYPPFLAGS = -n --line-marker-format=gfortran5

Waiting for a reply.
Thank you.


Sudarshan Behera
Graduate Student
Molecular Simulation Laboratory
JNCASR, Bengaluru, India-560064

Could you please also copy the whole output of the grompp?

Could you also try to use grompp with the following gmx_mpi_d:
/pfs/home/bala/Sudarshan/softwares/gromacs/build/bin/gmx_mpi_d

Just in case it is very bad idea to have build, source and installation directories in one place, i.e.
/pfs/home/bala/Sudarshan/softwares/gromacs/

Usually it is good to keep them all in separate places, for example:
installation directory is the same: /pfs/home/bala/Sudarshan/softwares/gromacs/
source directory: /pfs/home/bala/Sudarshan/source/gromacs/
and build directory: /pfs/home/bala/Sudarshan/build/gromacs/

Dear Dr. Dmitry,
Thank you for your reply.

As you suggested, I kept the build, source and installation directories in separate places while installation gromacs-2021.1-qmmm again. But I got the same error. I am pasting here the entire output of “grompp”:

:slight_smile: GROMACS - gmx grompp, 2021-dev-20200909-bc85c60-unknown (double precision) (-:

                        GROMACS is written by:
 Emile Apol      Rossen Apostolov      Paul Bauer     Herman J.C. Berendsen
Par Bjelkmar      Christian Blau   Viacheslav Bolnykh     Kevin Boyd    

Aldert van Buuren Rudi van Drunen Anton Feenstra Alan Gray
Gerrit Groenhof Anca Hamuraru Vincent Hindriksen M. Eric Irrgang
Aleksei Iupinov Christoph Junghans Joe Jordan Dimitrios Karkoulis
Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson
Justin A. Lemkul Viveca Lindahl Magnus Lundborg Erik Marklund
Pascal Merz Pieter Meulenhoff Teemu Murtola Szilard Pall
Sander Pronk Roland Schulz Michael Shirts Alexey Shvetsov
Alfons Sijbers Peter Tieleman Jon Vincent Teemu Virolainen
Christian Wennberg Maarten Wolf Artem Zhmurov
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) 2001-2019, 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 2021-dev-20200909-bc85c60-unknown (double precision)
Executable: /pfs/home/bala/Sudarshan/build/gromacs/bin/gmx_mpi_d
Data prefix: /pfs/home/bala/Sudarshan/source/gromacs (source tree)
Working dir: /pfs/home/bala/Sudarshan/Projects/LipA_Mutant/WT/Qm-MM/EM_mallige_test
Command line:
gmx_mpi_d grompp -f em-qmmm2.mdp -c …/EM/em.gro -p …/topol.top -n …/QM.ndx -o em-qmmm2.tpr

WARNING 1 [file em-qmmm2.mdp, line 27]:
Unknown left-hand ‘qmmm-active’ in parameter file

WARNING 2 [file em-qmmm2.mdp, line 27]:
Unknown left-hand ‘qmmm-qmgroup’ in parameter file

WARNING 3 [file em-qmmm2.mdp, line 27]:
Unknown left-hand ‘qmmm-qmmethod’ in parameter file

WARNING 4 [file em-qmmm2.mdp, line 27]:
Unknown left-hand ‘qmmm-qmcharge’ in parameter file

WARNING 5 [file em-qmmm2.mdp, line 27]:
Unknown left-hand ‘qmmm-qmmultiplicity’ in parameter file

NOTE 1 [file em-qmmm2.mdp]:
You have set rlist larger than the interaction cut-off, but you also have
verlet-buffer-tolerance > 0. Will set rlist using verlet-buffer-tolerance.

Setting the LD random seed to -15550786

Generated 2211 of the 2211 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5

Generated 2211 of the 2211 1-4 parameter combinations

Excluding 3 bonded neighbours molecule type ‘Protein_chain_A’

Excluding 2 bonded neighbours molecule type ‘SOL’

Excluding 2 bonded neighbours molecule type ‘SOL’

Excluding 1 bonded neighbours molecule type ‘CL’
Number of degrees of freedom in T-Coupling group rest is 67626.00
Calculating fourier grid dimensions for X Y Z
Using a fourier grid of 60x60x60, spacing 0.115 0.115 0.115

Estimate for the relative computational load of the PME mesh part: 0.20

This run will generate roughly 751 Mb of data

There was 1 note

There were 5 warnings


Program: gmx grompp, version 2021-dev-20200909-bc85c60-unknown
Source file: src/gromacs/gmxpreprocess/grompp.cpp (line 2382)

Fatal error:
Too many warnings (5).
If you are sure all warnings are harmless, use the -maxwarn option.

For more information and tips for troubleshooting, please check the GROMACS
website at Errors - Gromacs


MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
with errorcode 1.

NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
You may or may not see output from other processes, depending on
exactly when Open MPI kills them.

When I use “/pfs/home/bala/Sudarshan/softwares/gromacs/bin/gmx_mpi_d”, I get the same error.

I see the problem. You are compiling branch master instead of 2021.1-qmmm
Did you used git to download source?
If so then you forgot to switch branch to 2021.1-qmmm, from the INSTALL-dev:

If you want to clone whole repository, remember to checkout branch 2021.1-qmmm

this could be done with:
git checkout origin/2021.1-qmmm

Here is direct link to the branch if you want to download just 2021.1-qmmm:
https://gitlab.com/aracsmd/gromacs/-/archive/2021.1-qmmm/gromacs-2021.1-qmmm.tar.gz

Thank you for recongnizing the problem. I downloaded the gromacs-2021.1-qmm from the link you provided and installed. It is working fine now.

Thank you once again for helping me resolving the issue.