# Result analysis of QM/MM output from Gromacs\_CP2K **URL:** \ **Category:** QM/MM for Biomolecular Simulation\ **Created:** [March 5, 2022, 4:07pm UTC](https://ask.bioexcel.eu/t/result-analysis-of-qm-mm-output-from-gromacs-cp2k/3484 "2022-03-05T16:07:44Z")\ **Posts on this page:** 20\ **Page:** 1
**Author:** ![Rana1](https://avatars.discourse-cdn.com/v4/letter/r/d26b3c/32.png) [@Rana1](https://ask.bioexcel.eu/u/Rana1)\ **Post date:** [March 5, 2022, 4:07pm UTC](https://ask.bioexcel.eu/t/result-analysis-of-qm-mm-output-from-gromacs-cp2k/3484/1 "2022-03-05T16:07:44Z")
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 ---
**Author:** ![dmorozov](https://avatars.discourse-cdn.com/v4/letter/d/dec6dc/32.png) [@dmorozov](https://ask.bioexcel.eu/u/dmorozov)\ **Post date:** [March 7, 2022, 10:24am UTC](https://ask.bioexcel.eu/t/result-analysis-of-qm-mm-output-from-gromacs-cp2k/3484/2 "2022-03-07T10:24:52Z")
Hi, What kind of data you want to extract? Best, Dmitry ---
**Author:** ![Rana1](https://avatars.discourse-cdn.com/v4/letter/r/d26b3c/32.png) [@Rana1](https://ask.bioexcel.eu/u/Rana1)\ **Post date:** [March 7, 2022, 11:05am UTC](https://ask.bioexcel.eu/t/result-analysis-of-qm-mm-output-from-gromacs-cp2k/3484/3 "2022-03-07T11:05:00Z")
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? ---
**Author:** ![dmorozov](https://avatars.discourse-cdn.com/v4/letter/d/dec6dc/32.png) [@dmorozov](https://ask.bioexcel.eu/u/dmorozov)\ **Post date:** [March 7, 2022, 11:34am UTC](https://ask.bioexcel.eu/t/result-analysis-of-qm-mm-output-from-gromacs-cp2k/3484/4 "2022-03-07T11:34:23Z")
> 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](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: ```auto &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. ---
**Author:** ![Rana1](https://avatars.discourse-cdn.com/v4/letter/r/d26b3c/32.png) [@Rana1](https://ask.bioexcel.eu/u/Rana1)\ **Post date:** [March 7, 2022, 12:06pm UTC](https://ask.bioexcel.eu/t/result-analysis-of-qm-mm-output-from-gromacs-cp2k/3484/5 "2022-03-07T12:06:56Z")
Thanks a lot, Dmitry. ---
**Author:** ![Rana1](https://avatars.discourse-cdn.com/v4/letter/r/d26b3c/32.png) [@Rana1](https://ask.bioexcel.eu/u/Rana1)\ **Post date:** [March 8, 2022, 5:18pm UTC](https://ask.bioexcel.eu/t/result-analysis-of-qm-mm-output-from-gromacs-cp2k/3484/6 "2022-03-08T17:18:43Z")
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 ---
**Author:** ![dmorozov](https://avatars.discourse-cdn.com/v4/letter/d/dec6dc/32.png) [@dmorozov](https://ask.bioexcel.eu/u/dmorozov)\ **Post date:** [March 9, 2022, 8:08am UTC](https://ask.bioexcel.eu/t/result-analysis-of-qm-mm-output-from-gromacs-cp2k/3484/7 "2022-03-09T08:08:15Z")
> 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. ---
**Author:** ![Rana1](https://avatars.discourse-cdn.com/v4/letter/r/d26b3c/32.png) [@Rana1](https://ask.bioexcel.eu/u/Rana1)\ **Post date:** [March 27, 2022, 7:21pm UTC](https://ask.bioexcel.eu/t/result-analysis-of-qm-mm-output-from-gromacs-cp2k/3484/8 "2022-03-27T19:21:24Z")
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 ---
**Author:** ![dmorozov](https://avatars.discourse-cdn.com/v4/letter/d/dec6dc/32.png) [@dmorozov](https://ask.bioexcel.eu/u/dmorozov)\ **Post date:** [March 28, 2022, 7:01am UTC](https://ask.bioexcel.eu/t/result-analysis-of-qm-mm-output-from-gromacs-cp2k/3484/9 "2022-03-28T07:01:25Z")
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. ---
**Author:** ![Rana1](https://avatars.discourse-cdn.com/v4/letter/r/d26b3c/32.png) [@Rana1](https://ask.bioexcel.eu/u/Rana1)\ **Post date:** [April 3, 2022, 8:31pm UTC](https://ask.bioexcel.eu/t/result-analysis-of-qm-mm-output-from-gromacs-cp2k/3484/10 "2022-04-03T20:31:59Z")
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 ---
**Author:** ![dmorozov](https://avatars.discourse-cdn.com/v4/letter/d/dec6dc/32.png) [@dmorozov](https://ask.bioexcel.eu/u/dmorozov)\ **Post date:** [April 5, 2022, 1:53pm UTC](https://ask.bioexcel.eu/t/result-analysis-of-qm-mm-output-from-gromacs-cp2k/3484/11 "2022-04-05T13:53:41Z")
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](https://newtonx.org) ---
**Author:** ![Rana1](https://avatars.discourse-cdn.com/v4/letter/r/d26b3c/32.png) [@Rana1](https://ask.bioexcel.eu/u/Rana1)\ **Post date:** [April 6, 2022, 7:16am UTC](https://ask.bioexcel.eu/t/result-analysis-of-qm-mm-output-from-gromacs-cp2k/3484/12 "2022-04-06T07:16:27Z")
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) (-: GROMACS is written by: Andrey Alekseenko 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 Gilles Gouaillardet 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](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 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 [Common Errors — GROMACS webpage https://www.gromacs.org documentation](http://www.gromacs.org/Documentation/Errors) 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/](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/](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/](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 ---
**Author:** ![dmorozov](https://avatars.discourse-cdn.com/v4/letter/d/dec6dc/32.png) [@dmorozov](https://ask.bioexcel.eu/u/dmorozov)\ **Post date:** [April 7, 2022, 8:13am UTC](https://ask.bioexcel.eu/t/result-analysis-of-qm-mm-output-from-gromacs-cp2k/3484/13 "2022-04-07T08:13:27Z")
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 ---
**Author:** ![Rana1](https://avatars.discourse-cdn.com/v4/letter/r/d26b3c/32.png) [@Rana1](https://ask.bioexcel.eu/u/Rana1)\ **Post date:** [April 9, 2022, 1:25pm UTC](https://ask.bioexcel.eu/t/result-analysis-of-qm-mm-output-from-gromacs-cp2k/3484/14 "2022-04-09T13:25:38Z")
Hello Dmitry, Kindly find the files you asked for at the following link:-[gmx\_cp2k\_files.zip - Google Drive](https://drive.google.com/file/d/1rwC68es5zWaYB98EsBuzDc4uo8ebp-ol/view?usp=sharing) 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 ---
**Author:** ![dmorozov](https://avatars.discourse-cdn.com/v4/letter/d/dec6dc/32.png) [@dmorozov](https://ask.bioexcel.eu/u/dmorozov)\ **Post date:** [April 10, 2022, 9:06am UTC](https://ask.bioexcel.eu/t/result-analysis-of-qm-mm-output-from-gromacs-cp2k/3484/15 "2022-04-10T09:06:49Z")
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](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](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: > **[GitHub - bioexcel/gromacs-2022-cp2k-tutorial: Sample inputs and tutorial for...](https://github.com/bioexcel/gromacs-2022-cp2k-tutorial)** > > Sample inputs and tutorial for GROMACS-2022/CP2K QMMM interface - GitHub - bioexcel/gromacs-2022-cp2k-tutorial: Sample inputs and tutorial for GROMACS-2022/CP2K QMMM interface Dmitry ---
**Author:** ![Rana1](https://avatars.discourse-cdn.com/v4/letter/r/d26b3c/32.png) [@Rana1](https://ask.bioexcel.eu/u/Rana1)\ **Post date:** [April 17, 2022, 6:57pm UTC](https://ask.bioexcel.eu/t/result-analysis-of-qm-mm-output-from-gromacs-cp2k/3484/16 "2022-04-17T18:57:07Z")
Hello Dmitry, I had installed gromacs 2021.1 version from the following link:- [Files · 2021.1-qmmm · Dmitry Morozov / CP2KInterface · GitLab](https://gitlab.com/aracsmd/gromacs/-/tree/2021.1-qmmm) 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 ---
**Author:** ![dmorozov](https://avatars.discourse-cdn.com/v4/letter/d/dec6dc/32.png) [@dmorozov](https://ask.bioexcel.eu/u/dmorozov)\ **Post date:** [April 18, 2022, 7:45am UTC](https://ask.bioexcel.eu/t/result-analysis-of-qm-mm-output-from-gromacs-cp2k/3484/17 "2022-04-18T07:45:02Z")
Hi Ranabir, > I had installed gromacs 2021.1 version from the following link:- [Files · 2021.1-qmmm · Dmitry Morozov / CP2KInterface · GitLab](https://gitlab.com/aracsmd/gromacs/-/tree/2021.1-qmmm) 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. ---
**Author:** ![Pallavi0707](https://avatars.discourse-cdn.com/v4/letter/p/eb8c5e/32.png) [@Pallavi0707](https://ask.bioexcel.eu/u/Pallavi0707)\ **Post date:** [April 29, 2022, 5:35am UTC](https://ask.bioexcel.eu/t/result-analysis-of-qm-mm-output-from-gromacs-cp2k/3484/18 "2022-04-29T05:35:14Z")
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…?? ---
**Author:** ![dmorozov](https://avatars.discourse-cdn.com/v4/letter/d/dec6dc/32.png) [@dmorozov](https://ask.bioexcel.eu/u/dmorozov)\ **Post date:** [April 29, 2022, 4:34pm UTC](https://ask.bioexcel.eu/t/result-analysis-of-qm-mm-output-from-gromacs-cp2k/3484/19 "2022-04-29T16:34:11Z")
What is the problem? Could you attach any files? ---
**Author:** ![Pallavi0707](https://avatars.discourse-cdn.com/v4/letter/p/eb8c5e/32.png) [@Pallavi0707](https://ask.bioexcel.eu/u/Pallavi0707)\ **Post date:** [April 30, 2022, 6:42am UTC](https://ask.bioexcel.eu/t/result-analysis-of-qm-mm-output-from-gromacs-cp2k/3484/20 "2022-04-30T06:42:21Z")
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’ ![Screenshot (219)](https://europe1.discourse-cdn.com/flex013/uploads/bioexcel/original/1X/67aaef042b99f1f52c626fa12a2d5988c4abf4ea.png) [Next page](https://ask.bioexcel.eu/t/result-analysis-of-qm-mm-output-from-gromacs-cp2k/3484.md?page=2)