# \#gmx-grompp **URL:** https://gromacs.bioexcel.eu/tag/gmx-grompp/71.md [Latest](https://gromacs.bioexcel.eu/latest.md) · [Categories](https://gromacs.bioexcel.eu/categories.md) · [Tags](https://gromacs.bioexcel.eu/tags.md) --- ## [Ligand jumping from the box](https://gromacs.bioexcel.eu/t/ligand-jumping-from-the-box/12851)
**Author:** [@Mashi](https://gromacs.bioexcel.eu/u/Mashi)\ **Replies:** 0\ **Last updated:** [October 30, 2025, 11:42am UTC](https://gromacs.bioexcel.eu/t/ligand-jumping-from-the-box/12851 "2025-10-30T11:42:43Z")
I have started the MD simulation of a protein ligand interaction for 100ns. first, i created a box for the protein in center then added the ligand molecules and after the neutralization, i saw all of my protein, ligand a… --- ## [Protein deformation after energy minimization](https://gromacs.bioexcel.eu/t/protein-deformation-after-energy-minimization/11650)
**Author:** [@nhina](https://gromacs.bioexcel.eu/u/nhina)\ **Replies:** 0\ **Last updated:** [February 28, 2025, 10:16am UTC](https://gromacs.bioexcel.eu/t/protein-deformation-after-energy-minimization/11650 "2025-02-28T10:16:58Z")
GROMACS version: 2019 GROMACS modification: Yes/No I am doing MD simulation of protein\_DNA\_ligand system and stopped at energy minimization step, I use gromacs 2019, forcefield AMBER99SB-ILDN, water model TIP3P. After… --- ## [No default improper dihedral types in Amber ff14sb-OL21 for DNA simulations](https://gromacs.bioexcel.eu/t/no-default-improper-dihedral-types-in-amber-ff14sb-ol21-for-dna-simulations/10813)
**Author:** [@TGaziri](https://gromacs.bioexcel.eu/u/TGaziri)\ **Replies:** 2\ **Last updated:** [December 22, 2024, 12:33am UTC](https://gromacs.bioexcel.eu/t/no-default-improper-dihedral-types-in-amber-ff14sb-ol21-for-dna-simulations/10813 "2024-12-22T00:33:12Z")
GROMACS version: 2022.4 GROMACS modification: No Hello, I’m trying to set up a DNA simulation with Amber OL21, using the Gromacs port of the ff14sb-OL21 forcefield. But after I created the topology I got a bunch of th… --- ## [Topology file does not match](https://gromacs.bioexcel.eu/t/topology-file-does-not-match/10641)
**Author:** [@nhina](https://gromacs.bioexcel.eu/u/nhina)\ **Replies:** 2\ **Last updated:** [November 26, 2024, 6:31pm UTC](https://gromacs.bioexcel.eu/t/topology-file-does-not-match/10641 "2024-11-26T18:31:01Z")
GROMACS version: 2019.6 Hi guys, I am doing MD simulation with OPLS-AA forcefield for protein\_ligand system. The ligand is parameterized by webtools LigGenPar. I am adding ions to the system after solvate step. When r… --- ## [Energy Interaction between two groups](https://gromacs.bioexcel.eu/t/energy-interaction-between-two-groups/9827)
**Author:** [@shivam1](https://gromacs.bioexcel.eu/u/shivam1)\ **Replies:** 11\ **Last updated:** [October 8, 2024, 7:23am UTC](https://gromacs.bioexcel.eu/t/energy-interaction-between-two-groups/9827 "2024-10-08T07:23:02Z")
GROMACS version: GROMACS modification: Yes/No Hi @jalemkul @hess I want to calculated the energy interaction between two protein groups upon MD simulation is finished. My question is: which .gro and .cpt file should I… --- ## [For two ligand and a complex molecular dynamics simulation in GROMACS](https://gromacs.bioexcel.eu/t/for-two-ligand-and-a-complex-molecular-dynamics-simulation-in-gromacs/9880)
**Author:** [@Kirtiman07](https://gromacs.bioexcel.eu/u/Kirtiman07)\ **Replies:** 2\ **Last updated:** [August 15, 2024, 7:34am UTC](https://gromacs.bioexcel.eu/t/for-two-ligand-and-a-complex-molecular-dynamics-simulation-in-gromacs/9880 "2024-08-15T07:34:52Z")
Program: gmx genion, version 2020.1-Ubuntu-2020.1-1 Source file: src/gromacs/gmxpreprocess/genion.cpp (line 155) Fatal error: No more replaceable solvent! so how can i over come this problem. this error is showi… --- ## [Minimization issue](https://gromacs.bioexcel.eu/t/minimization-issue/9769)
**Author:** [@Fayaz](https://gromacs.bioexcel.eu/u/Fayaz)\ **Replies:** 4\ **Last updated:** [August 8, 2024, 5:54am UTC](https://gromacs.bioexcel.eu/t/minimization-issue/9769 "2024-08-08T05:54:47Z")
hello i am a new user. I am doing pure simulation of phospholipids , membrane contains 100 dop molecules and 2000 water molecules so each layer contains 50 dop molecules and 1000 water molecules i face this issue how t… --- ## [Gmx grompp -f minim.mdp -c DopGte.pdb -p topol.top -o dppc.tpr?](https://gromacs.bioexcel.eu/t/gmx-grompp-f-minim-mdp-c-dopgte-pdb-p-topol-top-o-dppc-tpr/9497)
**Author:** [@Fayaz](https://gromacs.bioexcel.eu/u/Fayaz)\ **Replies:** 14\ **Last updated:** [June 27, 2024, 6:10pm UTC](https://gromacs.bioexcel.eu/t/gmx-grompp-f-minim-mdp-c-dopgte-pdb-p-topol-top-o-dppc-tpr/9497 "2024-06-27T18:10:45Z")
Hello, anyone help me to solve this issue gmx grompp -f minim.mdp -c DopGte.pdb -p topol.top -o dppc.tpr Ignoring obsolete mdp entry ‘ns\_type’ NOTE 1 \[file minim.mdp\]: With Verlet lists the optimal nstlist is \>= 10, … --- ## [No default Bond types, U-B types](https://gromacs.bioexcel.eu/t/no-default-bond-types-u-b-types/9404)
**Author:** [@Fayaz](https://gromacs.bioexcel.eu/u/Fayaz)\ **Replies:** 0\ **Last updated:** [June 15, 2024, 6:01pm UTC](https://gromacs.bioexcel.eu/t/no-default-bond-types-u-b-types/9404 "2024-06-15T18:01:24Z")
Hello, I have attached a picture of errors. Can anyone guide how to fix this problem? --- ## [Segmentation fault -error](https://gromacs.bioexcel.eu/t/segmentation-fault-error/8496)
**Author:** [@IshaChauhan](https://gromacs.bioexcel.eu/u/IshaChauhan)\ **Replies:** 2\ **Last updated:** [March 4, 2024, 10:03am UTC](https://gromacs.bioexcel.eu/t/segmentation-fault-error/8496 "2024-03-04T10:03:24Z")
GROMACS version: :-) GROMACS - gmx grompp, 2024 (-: GROMACS modification: Yes/No Here post your question /usr/local/gromacs-2024/bin/gmx grompp -f minim.mdp -c bblcelbox3.gro -p topol.top -o min.tpr :-) GROMACS - gmx… --- ## [GPU support and installation](https://gromacs.bioexcel.eu/t/gpu-support-and-installation/8083)
**Author:** [@tebg](https://gromacs.bioexcel.eu/u/tebg)\ **Replies:** 2\ **Last updated:** [January 20, 2024, 8:42am UTC](https://gromacs.bioexcel.eu/t/gpu-support-and-installation/8083 "2024-01-20T08:42:03Z")
GROMACS version: 2023.3 GROMACS modification: Yes (I think??) I’ve just started setting up a new PC with the main goal of running MD simulations, and I’m trying to test out a simple membrane simulation generated by CHA… --- ## [Grommp fatal error](https://gromacs.bioexcel.eu/t/grommp-fatal-error/7801)
**Author:** [@mohon](https://gromacs.bioexcel.eu/u/mohon)\ **Replies:** 1\ **Last updated:** [December 6, 2023, 3:38pm UTC](https://gromacs.bioexcel.eu/t/grommp-fatal-error/7801 "2023-12-06T15:38:45Z")
GROMACS version:2023.2 GROMACS modification: Yes I am simulating HDAC11 protein with its known inhibitor FT895 in GROMACS 2023.2. As HDAC11 has zinc, I modified the forcefield in amber-ildn described in the paper https…