# Drude-compatible GROMACS code 2 **URL:** \ **Category:** User discussions\ **Created:** [November 19, 2020, 6:01pm UTC](https://gromacs.bioexcel.eu/t/drude-compatible-gromacs-code-2/1123 "2020-11-19T18:01:53Z")\ **Posts on this page:** 7\ **Page:** 1
**Author:** ![bellafrizzo](https://avatars.discourse-cdn.com/v4/letter/b/b487fb/32.png) [@bellafrizzo](https://gromacs.bioexcel.eu/u/bellafrizzo)\ **Post date:** [November 19, 2020, 6:01pm UTC](https://gromacs.bioexcel.eu/t/drude-compatible-gromacs-code-2/1123/1 "2020-11-19T18:01:53Z")
Hello everyone, during the NVT equilibration of my system I have a segmentation fault, even with a single molecule in a box. My system is a tetradecane molecule I have readapted as a residue from CHARMM FF. I guess the problem is the topology, but I don’t know what. Thank you in advance Matteo ---
**Author:** ![bellafrizzo](https://avatars.discourse-cdn.com/v4/letter/b/b487fb/32.png) [@bellafrizzo](https://gromacs.bioexcel.eu/u/bellafrizzo)\ **Post date:** [November 19, 2020, 7:22pm UTC](https://gromacs.bioexcel.eu/t/drude-compatible-gromacs-code-2/1123/2 "2020-11-19T19:22:15Z")
Actually this is the .log file: * * * There are: 7788 Atoms There are: 2478 Shells Will never predict shell positions Atom distribution over 24 domains: av 427 stddev 47 min 342 max 485 Initial temperature: -nan K Started mdrun on rank 0 Thu Nov 19 20:02:36 2020 Step Time 0 0.00000 * * * And this is the fatal error: * * * Fatal error: 1979 particles communicated to PME rank 2 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension x. This usually means that your system is not well equilibrated. * * * ---
**Author:** ![jalemkul](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/jalemkul/32/18_2.png) [@jalemkul](https://gromacs.bioexcel.eu/u/jalemkul)\ **Post date:** [November 19, 2020, 7:37pm UTC](https://gromacs.bioexcel.eu/t/drude-compatible-gromacs-code-2/1123/3 "2020-11-19T19:37:29Z")
If a single molecule fails then your topology is unsound. Parametrizing polarizable molecules requires great care and it is easy to generate a set of parameters that “works” (i.e. agrees with target data) but is ultimately unsuitable for a simulation due to overpolarization issues. ---
**Author:** ![bellafrizzo](https://avatars.discourse-cdn.com/v4/letter/b/b487fb/32.png) [@bellafrizzo](https://gromacs.bioexcel.eu/u/bellafrizzo)\ **Post date:** [November 19, 2020, 7:52pm UTC](https://gromacs.bioexcel.eu/t/drude-compatible-gromacs-code-2/1123/4 "2020-11-19T19:52:57Z")
Thank you for the answer. What about the charmm2gmx phyton script to convert? Is it available? ---
**Author:** ![jalemkul](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/jalemkul/32/18_2.png) [@jalemkul](https://gromacs.bioexcel.eu/u/jalemkul)\ **Post date:** [November 19, 2020, 8:03pm UTC](https://gromacs.bioexcel.eu/t/drude-compatible-gromacs-code-2/1123/5 "2020-11-19T20:03:49Z")
That won’t work for Drude, and we do not have generally available utilities for any such conversion. ---
**Author:** ![bellafrizzo](https://avatars.discourse-cdn.com/v4/letter/b/b487fb/32.png) [@bellafrizzo](https://gromacs.bioexcel.eu/u/bellafrizzo)\ **Post date:** [November 20, 2020, 8:29am UTC](https://gromacs.bioexcel.eu/t/drude-compatible-gromacs-code-2/1123/6 "2020-11-20T08:29:54Z")
I mean the header in aminoacids.rtp says: ; This force field generated by charmm2gmx\_v5.2.multiple.drude.py from ; the following Drude force field files: ; 2013f protein and model compounds ; 2017c DNA/RNA ; 2017c lipid ; 2018a carbohydrate ---
**Author:** ![jalemkul](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/jalemkul/32/18_2.png) [@jalemkul](https://gromacs.bioexcel.eu/u/jalemkul)\ **Post date:** [November 20, 2020, 3:34pm UTC](https://gromacs.bioexcel.eu/t/drude-compatible-gromacs-code-2/1123/7 "2020-11-20T15:34:21Z")
I have scripts that convert the entire force field to GROMACS format. I do not have scripts that generate Drude topologies or that are suited to standalone conversions of CHARMM RTF entries to GROMACS residue definitions.