# GROMACS **URL:** https://ask.bioexcel.eu/c/gromacs/5.md [Latest](https://ask.bioexcel.eu/latest.md) · [Categories](https://ask.bioexcel.eu/categories.md) · [Tags](https://ask.bioexcel.eu/tags.md) --- ## [About the GROMACS category](https://ask.bioexcel.eu/t/about-the-gromacs-category/25)
**Author:** [@rossen](https://ask.bioexcel.eu/u/rossen)\ **Replies:** 2\ **Last updated:** [May 11, 2016, 3:22pm UTC](https://ask.bioexcel.eu/t/about-the-gromacs-category/25 "2016-05-11T15:22:37Z")
Find the GROMACS forum at http://gromacs.bioexcel.eu --- ## [Protein structure preparation](https://ask.bioexcel.eu/t/protein-structure-preparation/1881)
**Author:** [@Panos\_K](https://ask.bioexcel.eu/u/Panos_K)\ **Replies:** 1\ **Last updated:** [April 8, 2020, 1:39pm UTC](https://ask.bioexcel.eu/t/protein-structure-preparation/1881 "2020-04-08T13:39:08Z")
Hello forum, I would like to know if there is an established procedure for dealing with structures having a high net-charge. I am not a chem, but I understand that this will mess with the simulation. I am aware that cou… --- ## [Base Trajectory](https://ask.bioexcel.eu/t/base-trajectory/1530)
**Author:** [@MARYMSH](https://ask.bioexcel.eu/u/MARYMSH)\ **Replies:** 1\ **Last updated:** [May 22, 2019, 5:52pm UTC](https://ask.bioexcel.eu/t/base-trajectory/1530 "2019-05-22T17:52:47Z")
Dear I need to use Gromacs software, but tool icon is inactive and can’t be changed! Thank you so much. Best regards --- ## [Protein-ligand Molecular dynamics using gromacs](https://ask.bioexcel.eu/t/protein-ligand-molecular-dynamics-using-gromacs/1432)
**Author:** [@harshitha](https://ask.bioexcel.eu/u/harshitha)\ **Replies:** 1\ **Last updated:** [March 12, 2019, 10:11am UTC](https://ask.bioexcel.eu/t/protein-ligand-molecular-dynamics-using-gromacs/1432 "2019-03-12T10:11:46Z")
How to prepare hybrid forcefield in case of protein ligand simulation --- ## [Steered molecular dynamics](https://ask.bioexcel.eu/t/steered-molecular-dynamics/1403)
**Author:** [@harshitha](https://ask.bioexcel.eu/u/harshitha)\ **Replies:** 1\ **Last updated:** [February 4, 2019, 1:40pm UTC](https://ask.bioexcel.eu/t/steered-molecular-dynamics/1403 "2019-02-04T13:40:53Z")
In gromacs umbrella sampling as it mentioned in pull code that pull along the z co-ordinate , but in my case the molecules pulling over the protein is not in a x axis ,y axis and z axis .it should be pull in between the … --- ## [GPU change, recompile Gromacs?](https://ask.bioexcel.eu/t/gpu-change-recompile-gromacs/1071)
**Author:** [@hovo1990](https://ask.bioexcel.eu/u/hovo1990)\ **Replies:** 2\ **Last updated:** [July 19, 2018, 6:02am UTC](https://ask.bioexcel.eu/t/gpu-change-recompile-gromacs/1071 "2018-07-19T06:02:54Z")
Hello everyone, My computer characteristics used to be: Ryzen 1700 8 GB RAM Nvidia GTX 960 Gromacs 2018.2 uses 100% of the CPU and 93-97% of the GPU for a protein system solvated in water and counter ions(65000 atom… --- ## [Trouble installing Gromacs](https://ask.bioexcel.eu/t/trouble-installing-gromacs/696)
**Author:** [@Diogo](https://ask.bioexcel.eu/u/Diogo)\ **Replies:** 3\ **Last updated:** [July 18, 2018, 1:58pm UTC](https://ask.bioexcel.eu/t/trouble-installing-gromacs/696 "2018-07-18T13:58:34Z")
I’ve tried installing using linux in a VM, I follow all the steps of the site however it always results in the same problem. Is there any coherent tutorial I can follow? --- ## [Membrane simulation](https://ask.bioexcel.eu/t/membrane-simulation/410)
**Author:** [@HosseinLanjanian](https://ask.bioexcel.eu/u/HosseinLanjanian)\ **Replies:** 3\ **Last updated:** [July 24, 2017, 8:22am UTC](https://ask.bioexcel.eu/t/membrane-simulation/410 "2017-07-24T08:22:56Z")
Dear All Hi I am working on a membrane protein. I created a membrane using VMD "membrane builder" and merged it with the protein pdb file by "Merge Structures" of VMD, for the rest of works I tried to use gromacs. My ide… --- ## [Moving atoms between repartition and force evaluation](https://ask.bioexcel.eu/t/moving-atoms-between-repartition-and-force-evaluation/308)
**Author:** [@ibethune](https://ask.bioexcel.eu/u/ibethune)\ **Replies:** 2\ **Last updated:** [March 7, 2017, 9:10am UTC](https://ask.bioexcel.eu/t/moving-atoms-between-repartition-and-force-evaluation/308 "2017-03-07T09:10:46Z")
Hi Gromacs developers, I am hacking some experimental integrators into GROMACS (working with gromacs 5.0.2 for some historical reasons). In my scheme between the repartitioning at the start of the step ( dd\_partition\_… --- ## [BioExcel Webinar #2: Performance tuning and optimization of GROMACS webinar](https://ask.bioexcel.eu/t/bioexcel-webinar-2-performance-tuning-and-optimization-of-gromacs-webinar/88)
**Author:** [@mabraham](https://ask.bioexcel.eu/u/mabraham)\ **Replies:** 0\ **Last updated:** [May 11, 2016, 3:10pm UTC](https://ask.bioexcel.eu/t/bioexcel-webinar-2-performance-tuning-and-optimization-of-gromacs-webinar/88 "2016-05-11T15:10:40Z")
Thanks for coming along today. Please feel free to ask questions here, or in a new topic. \[:slight\_smile:\] You can find the webinar and my slides at http://bioexcel.eu/webinar-performance-tuning-and-optimization-of-gro… --- ## [AMBER force field](https://ask.bioexcel.eu/t/amber-force-field/210)
**Author:** [@Panos\_K](https://ask.bioexcel.eu/u/Panos_K)\ **Replies:** 2\ **Last updated:** [September 26, 2016, 1:51pm UTC](https://ask.bioexcel.eu/t/amber-force-field/210 "2016-09-26T13:51:29Z")
Hello, I need to perform a MD simulation using GROMACS and I need to use AMBER force field. I see that 99sb-ildn is the most recent version included in the package. I also found a page with user-contributed ports of m… --- ## [Regarding minimization of edited structures](https://ask.bioexcel.eu/t/regarding-minimization-of-edited-structures/159)
**Author:** [@Panos\_K](https://ask.bioexcel.eu/u/Panos_K)\ **Replies:** 1\ **Last updated:** [July 17, 2016, 1:23pm UTC](https://ask.bioexcel.eu/t/regarding-minimization-of-edited-structures/159 "2016-07-17T13:23:23Z")
Dear admins, Supposing that we have a minimized structure with GROMACS, I wondered if a second minimization is necessary when we e.g. change a residue in a protein. I would like to know if this case is different betwee…