# Third party tools and files **URL:** https://gromacs.bioexcel.eu/c/third-party-tools-and-files/8.md?page=1 [Latest](https://gromacs.bioexcel.eu/latest.md) · [Categories](https://gromacs.bioexcel.eu/categories.md) · [Tags](https://gromacs.bioexcel.eu/tags.md) **Page:** 2 --- ## [Making densities (multimers/aggregates/objects) whole over PBC](https://gromacs.bioexcel.eu/t/making-densities-multimers-aggregates-objects-whole-over-pbc/3635)
**Author:** [@Bart](https://gromacs.bioexcel.eu/u/Bart)\ **Replies:** 0\ **Last updated:** [February 9, 2022, 1:25pm UTC](https://gromacs.bioexcel.eu/t/making-densities-multimers-aggregates-objects-whole-over-pbc/3635 "2022-02-09T13:25:00Z")
MDVWhole can be used to make broken segments over PBC whole. All you need is a coordinate and or trajectory file. It does not make any copies of the box and can handle an arbitrary amount of consecutive PBC crossings. Ma… --- ## [GROMACS implementation of the AMBER99SB-UCB force field](https://gromacs.bioexcel.eu/t/gromacs-implementation-of-the-amber99sb-ucb-force-field/2487)
**Author:** [@bkav](https://gromacs.bioexcel.eu/u/bkav)\ **Replies:** 0\ **Last updated:** [July 9, 2021, 5:39pm UTC](https://gromacs.bioexcel.eu/t/gromacs-implementation-of-the-amber99sb-ucb-force-field/2487 "2021-07-09T17:39:04Z")
The GROMACS implementation of the AMBER99SB-UCB force field. are the two reference papers for this force field. Link: GitHub - strodel-group/AMBER99SB-UCB Contact person (name and email address): Birgit Strodel b.s… --- ## [GMXRC for the Fish shell](https://gromacs.bioexcel.eu/t/gmxrc-for-the-fish-shell/2873)
**Author:** [@pjohansson](https://gromacs.bioexcel.eu/u/pjohansson)\ **Replies:** 0\ **Last updated:** [September 27, 2021, 8:37am UTC](https://gromacs.bioexcel.eu/t/gmxrc-for-the-fish-shell/2873 "2021-09-27T08:37:49Z")
Brief description of tools/files: Gromacs installs a few GMXRC files alongside its binary in $GROMACS\_DIR/bin. By sourcing the appropriate file for your shell, the appropriate PATH variables (and a few Gromacs specific o… --- ## [QM/MM with xtb and Turbomole](https://gromacs.bioexcel.eu/t/qm-mm-with-xtb-and-turbomole/2232)
**Author:** [@rmera](https://gromacs.bioexcel.eu/u/rmera)\ **Replies:** 0\ **Last updated:** [May 27, 2021, 11:47am UTC](https://gromacs.bioexcel.eu/t/qm-mm-with-xtb-and-turbomole/2232 "2021-05-27T11:47:29Z")
Dear all, A while ago I wrote a small tool that translates a subsets of inputs/outputs between Turbomole and Orca, so that the former can be used on any QM/MM engine that supports the latter. I recently added support fo… --- ## [Software for running NMR refinement in GROMACS](https://gromacs.bioexcel.eu/t/software-for-running-nmr-refinement-in-gromacs/1851)
**Author:** [@dspoel](https://gromacs.bioexcel.eu/u/dspoel)\ **Replies:** 0\ **Last updated:** [March 29, 2021, 10:25am UTC](https://gromacs.bioexcel.eu/t/software-for-running-nmr-refinement-in-gromacs/1851 "2021-03-29T10:25:44Z")
GROMACS version: 2020+ GROMACS modification: Yes/No Here post your question Dear all, we have just published a script to perform NMR refinement in GROMACS by converting a modern CIF file from the pdb to proper GROMAC… --- ## [GADDLE Maps, mapping Coarse Grained systems to Fully Atomistic](https://gromacs.bioexcel.eu/t/gaddle-maps-mapping-coarse-grained-systems-to-fully-atomistic/1706)
**Author:** [@hadrian](https://gromacs.bioexcel.eu/u/hadrian)\ **Replies:** 0\ **Last updated:** [March 8, 2021, 7:50am UTC](https://gromacs.bioexcel.eu/t/gaddle-maps-mapping-coarse-grained-systems-to-fully-atomistic/1706 "2021-03-08T07:50:12Z")
We are pleased to announce the release of the first open source version of the python module gaddlemaps, which implements the GADDLE Maps algorithm. This algorithm is able to map molecular systems between two different r… --- ## [Gromologist: a tool for Gromacs topology manipulation](https://gromacs.bioexcel.eu/t/gromologist-a-tool-for-gromacs-topology-manipulation/1364)
**Author:** [@milosz.wieczor](https://gromacs.bioexcel.eu/u/milosz.wieczor)\ **Replies:** 0\ **Last updated:** [December 31, 2020, 4:50pm UTC](https://gromacs.bioexcel.eu/t/gromologist-a-tool-for-gromacs-topology-manipulation/1364 "2020-12-31T16:50:31Z")
Hi, Working with Gromacs over the years, I’ve automatized a topology parser for personal use, and then implemented new features each time I needed one. What came out of this is Gromologist, a pip-installable library wit… --- ## [sol\_remover](https://gromacs.bioexcel.eu/t/sol-remover/909)
**Author:** [@fabiolol](https://gromacs.bioexcel.eu/u/fabiolol)\ **Replies:** 0\ **Last updated:** [October 5, 2020, 8:42am UTC](https://gromacs.bioexcel.eu/t/sol-remover/909 "2020-10-05T08:42:36Z")
sol\_remover is a Python script that removes all the specified residues from the given .gro file that are in a specific range. The intended use is to remove water molecules from the inside of the membrane. This is done … --- ## [Welcome to third party forum](https://gromacs.bioexcel.eu/t/welcome-to-third-party-forum/857)
**Author:** [@avilla](https://gromacs.bioexcel.eu/u/avilla)\ **Replies:** 0\ **Last updated:** [September 23, 2020, 10:17am UTC](https://gromacs.bioexcel.eu/t/welcome-to-third-party-forum/857 "2020-09-23T10:17:20Z")
Here you can post tools and files that you have developed. The tools and file (input files, topology, force fields database, and so on) have to be useful for the GROMACS community and not to have a commercial scope. The… [Previous page](https://gromacs.bioexcel.eu/c/third-party-tools-and-files/8.md)