Result analysis of QM/MM output from Gromacs_CP2K

Recently, I have run QM/MM simulation (Gromacs-CP2K) successfully but failed to analyze the data. I am new in QM/MM. Could you help to analyze data output from QM/MM simulation?

Kindly refer to any tutorial/ paper regarding that.

Thanking you
Ranabir

Hi,

What kind of data you want to extract?

Best,
Dmitry

Thanks for the reply.

I would like to calculate the reaction pathway, binding energy, Homo-Lumo orbitals energy gap (with image), etc.

Lastly, I would likely ask you that I have an intel i7 6 core processor and 16 GB ram. How large a biosystem (e.g. 50/100/150 atoms in QM region) can I run in my computer system?

calculate the reaction pathway

Use umbrella sampling for that. See Exercise 2 from this tutorial as an example: https://github.com/bioexcel/gromacs-2022-cp2k-tutorial

binding energy

I would suggest you to check which methods are typically used for your particular system to calculate that

Homo-Lumo orbitals energy gap (with image)

To do that you would need to use your own CP2K input file (See exercise 4 from the tutorial above)
For CP2K to print out orbitals you would need to add the following section to &FORCE_EVAL / &DFT:

    &PRINT
       &MO_CUBES                 
        NHOMO 1
        NLUMO 1
      &END MO_CUBES
    &END PRINT

Here NHOMO and NLUMO is the number of orbitals that CP2K will print in a standard *.cube format file

Lastly, I would likely ask you that I have an intel i7 6 core processor and 16 GB ram. How large a biosystem (e.g. 50/100/150 atoms in QM region) can I run in my computer system?

Very hard to say, not really big maybe around 30-40 atoms at the most.

Thanks a lot, Dmitry.

Hello sir,

I would like to know that is it possible to run QM/MM calculation with QMMM.inp file (Gromacs-cp2k interface generated) with an independent cp2k package.

Actually, my university HPC server does not have Gromacs-cp2k interface. It only has cp2k 8.2.

Therefore, I would like to generate a QMMM.inp file on my local PC with Gromacs-cp2k interface and later run it on HPC server.

Kindly give me some suggestion.

Thanking you,
Ranabir

I would like to know that is it possible to run QM/MM calculation with QMMM.inp file (Gromacs-cp2k interface generated) with an independent cp2k package.

Yes possible but it would be only energy for one point. I would suggest you to ask system administrators to install GROMACS-CP2K interface onto the HPC server, interface works with CP2K 8.2 well.

Dear Dmitry,

I have successfully run QM/MM using the Gromacs_CP2K interface (20 steps). It also generated (21+21) homo-lumo in *.cube format. As per your previous suggestion, the number of homo-lumo orbital was 1.

Kindly suggest to me which .cube file I should consider for analysis. Is it no. 21.cubic file? Also, is it ok to consider 1 orbital for analysis?

I am new to QM/MM simulation, so kindly help me to analyze the results.

Thanks
Ranabir

Sorry but this is completely arbitrary thing. It purely depends on which information you want to extract from the orbitals. By themselves orbitals is just showing probability of finding electron within their space. For example, if you want to see how charge moves around your system with excitation of electron then you would need to do TDDFT computation and check which orbitals are involved into transition from ground to excited state. On the other hand, if you want to check whether your molecule could be a conductor, then HOMO-LUMO energy gap should be checked…
So it really depends on your particular system and field of study.
To have a clue I suggest you to read other computational papers regarding your topic and check what typically peoples tend to extract from the simulations in that field.

Dear Dmitry,

Thanks for your kind suggestion. I am going through the papers and your tutorial materials. In the egfp_spec tutorial, you had shown how to calculate the absorption spectra of a molecule. Is it possible to calculate the electron properties of a molecule at a particular wavelength/ eV?

Actually, I am trying to simulate a molecule that is being reduced (experimentally) under 450 nm light emission. Could you give me some suggestions to modify TDDFPT section in cp2k input file?

Thanks again
Ranabir

Hi Ranabir,

For such kind of things you would need to perform excited-state dynamics, which is not possible now with the interface.
But there are some implementations of such methods form third parties, like this:
https://newtonx.org

Dear Dmitry,
Thanks again for your suggestion.

Also, I am trying to run egfp-spec (from bioexcel tutorials) but it has been stopped after running for few minutes in my institute’s HPC.

The slurm.out was as following:-

==========================================
SLURM_CLUSTER_NAME = param-shakti
SLURM_JOB_ACCOUNT = mahitoshmm
SLURM_JOB_ID = 734672
SLURM_JOB_NAME = Fgromacs_cp2k_qmmm
SLURM_JOB_NODELIST = cn[031,234,265]
SLURM_JOB_USER = mahitoshmm
SLURM_JOB_UID = 6555
SLURM_JOB_PARTITION = standard-low
SLURM_TASK_PID = 134933
SLURM_SUBMIT_DIR = /home/mahitoshmm/EGFP_Spec
SLURM_CPUS_ON_NODE = 16
SLURM_NTASKS = 12
SLURM_TASK_PID = 134933


WARNING: There was an error initializing an OpenFabrics device.

Local host: cn265
Local device: mlx5_0

  :-) GROMACS - gmx mdrun, 2021.2-dev-UNCHECKED (double precision) (-:

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GROMACS: gmx mdrun, version 2021.2-dev-UNCHECKED (double precision)
Executable: /home/mahitoshmm/gromacs-2021.1-qmmm-install/bin/gmx_mpi_d
Data prefix: /home/mahitoshmm/gromacs-2021.1-qmmm-install
Working dir: /home/mahitoshmm/EGFP_Spec
Command line:
gmx_mpi_d mdrun -v -deffnm egfp-spec

Back Off! I just backed up egfp-spec.log to ./#egfp-spec.log.4#
Reading file egfp-spec.tpr, VERSION 2021.2-dev-UNCHECKED (double precision)
Using 12 MPI processes

Non-default thread affinity set, disabling internal thread affinity

Using 4 OpenMP threads per MPI process

Back Off! I just backed up egfp-spec.xtc to ./#egfp-spec.xtc.4#

Back Off! I just backed up egfp-spec.trr to ./#egfp-spec.trr.4#

Back Off! I just backed up egfp-spec.edr to ./#egfp-spec.edr.4#
starting mdrun ‘Protein in water’
100 steps, 0.1 ps.
[cn031:135423] 11 more processes have sent help message help-mpi-btl-openib.txt / error in device init
[cn031:135423] Set MCA parameter “orte_base_help_aggregate” to 0 to see all help / error messages
cp2k_set_positions & cp2k_set_cell - DONE
cp2k_calc_energy_force - DONE
QMener=-113.178150851415

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

The egfp-spec.out(cp2k output file) was as follow:-

**** **** ****** ** PROGRAM STARTED AT 2022-04-05 01:10:50.272
***** ** *** *** ** PROGRAM STARTED ON cn031
** **** ****** PROGRAM STARTED BY mahitoshmm
***** ** ** ** ** PROGRAM PROCESS ID 132408
**** ** ******* ** PROGRAM STARTED IN /home/mahitoshmm/EGFP_Spec

CP2K| version string: CP2K version 8.2
CP2K| source code revision number: git:310b7ab
CP2K| cp2kflags: omp libint fftw3 libxc elpa parallel mpi3 scalapack cosma xsmm
CP2K| spglib sirius libvori libbqb
CP2K| is freely available from https://www.cp2k.org/
CP2K| Program compiled at Fri Mar 11 19:15:59 IST 2022
CP2K| Program compiled on login01.iitkgp.ac.in
CP2K| Program compiled for local
CP2K| Data directory path /home/mahitoshmm/cp2k-8.2/data
CP2K| Input file name egfp-spec.inp

**** **** ****** ** PROGRAM STARTED AT 2022-04-05 01:17:44.985
***** ** *** *** ** PROGRAM STARTED ON cn031
** **** ****** PROGRAM STARTED BY mahitoshmm
***** ** ** ** ** PROGRAM PROCESS ID 133706
**** ** ******* ** PROGRAM STARTED IN /home/mahitoshmm/EGFP_Spec

CP2K| version string: CP2K version 8.2
CP2K| source code revision number: git:310b7ab
CP2K| cp2kflags: omp libint fftw3 libxc elpa parallel mpi3 scalapack cosma xsmm
CP2K| spglib sirius libvori libbqb
CP2K| is freely available from https://www.cp2k.org/
CP2K| Program compiled at Fri Mar 11 19:15:59 IST 2022
CP2K| Program compiled on login01.iitkgp.ac.in
CP2K| Program compiled for local
CP2K| Data directory path /home/mahitoshmm/cp2k-8.2/data
CP2K| Input file name egfp-spec.inp

**** **** ****** ** PROGRAM STARTED AT 2022-04-05 01:21:45.350
***** ** *** *** ** PROGRAM STARTED ON cn031
** **** ****** PROGRAM STARTED BY mahitoshmm
***** ** ** ** ** PROGRAM PROCESS ID 134454
**** ** ******* ** PROGRAM STARTED IN /home/mahitoshmm/EGFP_Spec

CP2K| version string: CP2K version 8.2
CP2K| source code revision number: git:310b7ab
CP2K| cp2kflags: omp libint fftw3 libxc elpa parallel mpi3 scalapack cosma xsmm
CP2K| spglib sirius libvori libbqb
CP2K| is freely available from https://www.cp2k.org/
CP2K| Program compiled at Fri Mar 11 19:15:59 IST 2022
CP2K| Program compiled on login01.iitkgp.ac.in
CP2K| Program compiled for local
CP2K| Data directory path /home/mahitoshmm/cp2k-8.2/data
CP2K| Input file name egfp-spec.inp

Is there any problem in our HPC or else?

With regards
Ranabir

Hi Ranabir,

Could you please make an archive with you tpr file and output files for it and share somehow?
It is very hard to say what exactly happens, but seems like some problem with CP2K compilation. Could you also provide information on how did you compiled libcp2k and GROMACS. Especially I would be interested in command-line of cmake for GROMACS and install_cp2k_toolchain.sh for CP2K.

Best,
Dmitry

Hello Dmitry,

Kindly find the files you asked for at the following link:-gmx_cp2k_files.zip - Google Drive

Also, I would like to know that is it possible to run TDDFT calculation for the DNA-Ligand complex?

Actually, I have screened a molecule that is intercalating between DNA base pairs and activating toxicity (DNA damage) after exposure under visible light.

Is it possible to study (computationally) the DNA-Ligand complex electronic changes with light exposure?

I am new to QM/MM field. It will be a great help for my Ph.D. work if you can highlight it.

Thanks for your kind co-operation.

With regards,
Ranabir

Hi Ranabir,

You are using wrong version of the GROMACS (where did you found that?), please install the latest official release of GROMACS 2022:
https://manual.gromacs.org

And use the following installation guide:
https://manual.gromacs.org/current/install-guide/index.html#building-with-cp2k-qm-mm-support

The mdp parameters have also changed from thee version that you have tried to use to please follow the new tutorial:

Dmitry

Hello Dmitry,

I had installed gromacs 2021.1 version from the following link:- Files · 2021.1-qmmm · Dmitry Morozov / CP2KInterface · GitLab

I followed the INSTALL-dev instruction to interface between gromacs 2021.1-cp2k.

Is it ok if I generate necessary tpr files through the above mentioned gromacs-cp2k version?

Thanking you,
Ranabir

Hi Ranabir,

I had installed gromacs 2021.1 version from the following link:- Files · 2021.1-qmmm · Dmitry Morozov / CP2KInterface · GitLab

Not it is not correct version, please install right one using links in my previous message. That GROMACS 2022 with CP2K is the only supported version for now.

Is it ok if I generate necessary tpr files through the above mentioned gromacs-cp2k version?

No, they are not compatible.

Hello sir
I have to run the QM/MM sumulation (Gromacs-cp2k), I have Ubuntu OS in which I have installed Gromacs and cp2k. I’ve gone through the Practical: GROMACS + CP2K paper, but I’m unable to run it. can you please help me out with this…??

What is the problem? Could you attach any files?

I’m unable to do the first step only sir…
I tried to load the module but I’m getting error

~$ module load gromacs-cp2k
ERROR: Unable to locate a modulefile for ‘gromacs-cp2k’