# QM/MM for Biomolecular Simulation **URL:** https://ask.bioexcel.eu/c/qmmm-biosim/20.md [Latest](https://ask.bioexcel.eu/latest.md) · [Categories](https://ask.bioexcel.eu/categories.md) · [Tags](https://ask.bioexcel.eu/tags.md) --- ## [Guide to using CP2K for QM/MM simulation of biomolecular systems](https://ask.bioexcel.eu/t/guide-to-using-cp2k-for-qm-mm-simulation-of-biomolecular-systems/2746)
**Author:** [@aproeme](https://ask.bioexcel.eu/u/aproeme)\ **Replies:** 0\ **Last updated:** [December 18, 2020, 4:05pm UTC](https://ask.bioexcel.eu/t/guide-to-using-cp2k-for-qm-mm-simulation-of-biomolecular-systems/2746 "2020-12-18T16:05:55Z")
Anyone interested in using CP2K for QM/MM simulation of biomolecular systems may find the following guide useful: --- ## [About CP2K in Biomolecular Simulation](https://ask.bioexcel.eu/t/about-cp2k-in-biomolecular-simulation/1573)
**Author:** [@cblau](https://ask.bioexcel.eu/u/cblau)\ **Replies:** 5\ **Last updated:** [April 23, 2021, 8:29am UTC](https://ask.bioexcel.eu/t/about-cp2k-in-biomolecular-simulation/1573 "2021-04-23T08:29:13Z")
Challenges combining quantum mechanics and molecular mechanics using CP2K and GROMACS --- ## [QM/MM - Gromacs+CP2K ERROR](https://ask.bioexcel.eu/t/qm-mm-gromacs-cp2k-error/4658)
**Author:** [@isilayozturk](https://ask.bioexcel.eu/u/isilayozturk)\ **Replies:** 1\ **Last updated:** [November 23, 2023, 3:48pm UTC](https://ask.bioexcel.eu/t/qm-mm-gromacs-cp2k-error/4658 "2023-11-23T15:48:01Z")
Hello all, I am trying to apply QM/MM with Gromacs+CP2K interface but I have an error… I have Gallium and basic, N,O,H,C atoms. CP2K part is giving error. during energy minimization part. Probably gromacs part has a pro… --- ## [QM/MM CP2K- isotope](https://ask.bioexcel.eu/t/qm-mm-cp2k-isotope/4091)
**Author:** [@isilayozturk](https://ask.bioexcel.eu/u/isilayozturk)\ **Replies:** 3\ **Last updated:** [November 1, 2023, 12:54am UTC](https://ask.bioexcel.eu/t/qm-mm-cp2k-isotope/4091 "2023-11-01T00:54:27Z")
Can we specifically identify the metal of isotope when doing QM/MM in CP2K? Best! Işılay --- ## [QM/MM restart problem to generate cube files](https://ask.bioexcel.eu/t/qm-mm-restart-problem-to-generate-cube-files/4433)
**Author:** [@Rana1](https://ask.bioexcel.eu/u/Rana1)\ **Replies:** 0\ **Last updated:** [July 29, 2023, 6:12pm UTC](https://ask.bioexcel.eu/t/qm-mm-restart-problem-to-generate-cube-files/4433 "2023-07-29T18:12:48Z")
I am running 500 steps for a QM/MM simulation in Gromacs-cp2k 8.2 interface. I successfully ran 1st 100 steps in my HPC server. It generated 100 HOMO and 100 LUMO .cube files. My calculation was terminated after 100 step… --- ## [Reference for Gromacs-CP2K interface](https://ask.bioexcel.eu/t/reference-for-gromacs-cp2k-interface/4307)
**Author:** [@Rana1](https://ask.bioexcel.eu/u/Rana1)\ **Replies:** 1\ **Last updated:** [May 22, 2023, 6:08pm UTC](https://ask.bioexcel.eu/t/reference-for-gromacs-cp2k-interface/4307 "2023-05-22T18:08:13Z")
I have used gmx\_CP2K interface to run QM/MM TD-DFT calculation. Now, I would like to cite the tools in my research article. Could someone provide me with the info about how to cite it? Thanking you, Ranabir Majumder … --- ## [QM/MM simulation crashes with segmentation fault when running it a second time](https://ask.bioexcel.eu/t/qm-mm-simulation-crashes-with-segmentation-fault-when-running-it-a-second-time/4254)
**Author:** [@hpoggemann](https://ask.bioexcel.eu/u/hpoggemann)\ **Replies:** 2\ **Last updated:** [May 3, 2023, 7:58am UTC](https://ask.bioexcel.eu/t/qm-mm-simulation-crashes-with-segmentation-fault-when-running-it-a-second-time/4254 "2023-05-03T07:58:29Z")
Dear all, I am trying to run QM/MM simulations of an enzyme with an cysteine bound ferric heme in the centre and I came across a strange problem with my simulations: I did run an energy minimisation once that completed,… --- ## [Installation of GROMACS 2022.5 with CP2K 2023.1 using Intel compilers, mpi and mkl fails](https://ask.bioexcel.eu/t/installation-of-gromacs-2022-5-with-cp2k-2023-1-using-intel-compilers-mpi-and-mkl-fails/4238)
**Author:** [@rajib](https://ask.bioexcel.eu/u/rajib)\ **Replies:** 7\ **Last updated:** [April 20, 2023, 8:19pm UTC](https://ask.bioexcel.eu/t/installation-of-gromacs-2022-5-with-cp2k-2023-1-using-intel-compilers-mpi-and-mkl-fails/4238 "2023-04-20T20:19:47Z")
GROMACS version: 2022.5 CP2K Version: 2023.1 Compiler and library used: Intel compilers, mpi and mkl library Dear Community Members, I have followed the following website to install CP2K first: https://docs.bioexcel… --- ## [CP2K Tutorial - TS optimization for reaction mechanisms of enzymes](https://ask.bioexcel.eu/t/cp2k-tutorial-ts-optimization-for-reaction-mechanisms-of-enzymes/4217)
**Author:** [@arvpinto](https://ask.bioexcel.eu/u/arvpinto)\ **Replies:** 0\ **Last updated:** [March 24, 2023, 9:38am UTC](https://ask.bioexcel.eu/t/cp2k-tutorial-ts-optimization-for-reaction-mechanisms-of-enzymes/4217 "2023-03-24T09:38:58Z")
Dear CP2K users, I’ve recently developed a CP2K tutorial to find and optimize TS geometries for enzymatic mechanisms (using QM/MM). You can find it in the following public repository: This tutorial was made possible … --- ## [Installation of gromacs-2021.1-qmmm](https://ask.bioexcel.eu/t/installation-of-gromacs-2021-1-qmmm/2924)
**Author:** [@Sudchem](https://ask.bioexcel.eu/u/Sudchem)\ **Replies:** 21\ **Last updated:** [March 22, 2023, 1:58pm UTC](https://ask.bioexcel.eu/t/installation-of-gromacs-2021-1-qmmm/2924 "2023-03-22T13:58:12Z")
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… --- ## [Non-periodic QM region](https://ask.bioexcel.eu/t/non-periodic-qm-region/4080)
**Author:** [@Qinghua](https://ask.bioexcel.eu/u/Qinghua)\ **Replies:** 5\ **Last updated:** [January 24, 2023, 5:56pm UTC](https://ask.bioexcel.eu/t/non-periodic-qm-region/4080 "2023-01-24T17:56:35Z")
Hello, In my QM/MM simulation with Gromacs 2022.3 / CP2K 2023.1, I used non-periodic QM region in the CP2K input file, as I commented out the following lines in the QMMM block: ! &PERIODIC ! GMAX 1.0E+00 ! … --- ## [Checkpoint file during QM/MM simulation using GROMACS/CP2K](https://ask.bioexcel.eu/t/checkpoint-file-during-qm-mm-simulation-using-gromacs-cp2k/3947)
**Author:** [@Qinghua](https://ask.bioexcel.eu/u/Qinghua)\ **Replies:** 2\ **Last updated:** [October 24, 2022, 9:15am UTC](https://ask.bioexcel.eu/t/checkpoint-file-during-qm-mm-simulation-using-gromacs-cp2k/3947 "2022-10-24T09:15:28Z")
Hello, I am running QM/MM simulations with Gromacs v2022.3, CP2K v9.1 and PLUMED v2.8. For restart the simulation, I added “-cpt 2” in the command, which would write the checkpoint file every 2 minutes. But actually, a… --- ## [Result analysis of QM/MM output from Gromacs\_CP2K](https://ask.bioexcel.eu/t/result-analysis-of-qm-mm-output-from-gromacs-cp2k/3484)
**Author:** [@Rana1](https://ask.bioexcel.eu/u/Rana1)\ **Replies:** 52\ **Last updated:** [September 5, 2022, 7:06am UTC](https://ask.bioexcel.eu/t/result-analysis-of-qm-mm-output-from-gromacs-cp2k/3484 "2022-09-05T07:06:33Z")
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 regar… --- ## [QM/MM simulation crashed due to Segmentation fault](https://ask.bioexcel.eu/t/qm-mm-simulation-crashed-due-to-segmentation-fault/3751)
**Author:** [@Qinghua](https://ask.bioexcel.eu/u/Qinghua)\ **Replies:** 13\ **Last updated:** [June 28, 2022, 8:28am UTC](https://ask.bioexcel.eu/t/qm-mm-simulation-crashed-due-to-segmentation-fault/3751 "2022-06-28T08:28:31Z")
Hello everyone, I am trying to run a QM/MM minimization using Gromacs 2022.1/CP2K 9.1, but it failed due to Segmentation fault. Steepest Descents: Tolerance (Fmax) = 1.00000e+03 Number of steps = 1000 … --- ## [Out of memory- QM/MM](https://ask.bioexcel.eu/t/out-of-memory-qm-mm/3440)
**Author:** [@isilayozturk](https://ask.bioexcel.eu/u/isilayozturk)\ **Replies:** 13\ **Last updated:** [February 7, 2022, 7:55pm UTC](https://ask.bioexcel.eu/t/out-of-memory-qm-mm/3440 "2022-02-07T19:55:24Z")
Dear all, I defined to memory but many times It has given to the problem as an out of memory and my calculation has not been able to complete. I tried to so many things but I haven’t any idea what is wrong. I got this … --- ## [Constraint problems in GROMACS with CP2K QMMM interface](https://ask.bioexcel.eu/t/constraint-problems-in-gromacs-with-cp2k-qmmm-interface/3386)
**Author:** [@hij09373](https://ask.bioexcel.eu/u/hij09373)\ **Replies:** 3\ **Last updated:** [December 17, 2021, 1:01pm UTC](https://ask.bioexcel.eu/t/constraint-problems-in-gromacs-with-cp2k-qmmm-interface/3386 "2021-12-17T13:01:15Z")
Hi all, I have encountered problems with the interface between GROMACS and CP2K. I setup my calculation standardwise for GROMACS and did the whole standard procedure, minimization, NVT equilibration and NPT equilibratio… --- ## [Gromacs-2021.1-qmmm, Aborted (core dumped)](https://ask.bioexcel.eu/t/gromacs-2021-1-qmmm-aborted-core-dumped/3291)
**Author:** [@Rana1](https://ask.bioexcel.eu/u/Rana1)\ **Replies:** 1\ **Last updated:** [October 11, 2021, 9:16am UTC](https://ask.bioexcel.eu/t/gromacs-2021-1-qmmm-aborted-core-dumped/3291 "2021-10-11T09:16:30Z")
I am facing a problem running QMMM calculation using gromacs-2021.1-qmmm (cp2k). It is showing Aborted (core dumped) in QM production run through gromacs. Kindly, help. --- ## [General questions for CP2K new user](https://ask.bioexcel.eu/t/general-questions-for-cp2k-new-user/3203)
**Author:** [@MarioMoser](https://ask.bioexcel.eu/u/MarioMoser)\ **Replies:** 2\ **Last updated:** [August 19, 2021, 11:44pm UTC](https://ask.bioexcel.eu/t/general-questions-for-cp2k-new-user/3203 "2021-08-19T23:44:26Z")
Hello my name is Mario i just graduated from Strasbourg Master 2 chemoinformatics and i would like to use CP2K for QM/MM calculations on biomolecular systems. The ultimate goal would be to simualte a system composed of… --- ## [QM/MM Umbrella Sampling: How to generate initial conformations?](https://ask.bioexcel.eu/t/qm-mm-umbrella-sampling-how-to-generate-initial-conformations/2899)
**Author:** [@longorefisher](https://ask.bioexcel.eu/u/longorefisher)\ **Replies:** 1\ **Last updated:** [April 27, 2021, 1:43pm UTC](https://ask.bioexcel.eu/t/qm-mm-umbrella-sampling-how-to-generate-initial-conformations/2899 "2021-04-27T13:43:22Z")
Hi all, I was fortunate enough to attend a recent CP2K/GROMACS course and am now trying to test out the interface on some other toy systems. The reaction I’m trying to model is abstraction of the hydrogen from a carbon … --- ## [Error on the CP2K QM/MM tutorial on biochemical systems](https://ask.bioexcel.eu/t/error-on-the-cp2k-qm-mm-tutorial-on-biochemical-systems/1583)
**Author:** [@sllabres](https://ask.bioexcel.eu/u/sllabres)\ **Replies:** 2\ **Last updated:** [June 3, 2019, 4:46pm UTC](https://ask.bioexcel.eu/t/error-on-the-cp2k-qm-mm-tutorial-on-biochemical-systems/1583 "2019-06-03T16:46:31Z")
Hello, I am running the QM/MM tutorial on chorismate mutate as posted on the CP2K webpage (www.cp2k.org/howto:biochem\_qmmm). I managed to run the first steps including MM minimisation and MM equilibration (NVT and NPT).…