# \#constraint-algorithms **URL:** https://gromacs.bioexcel.eu/tag/constraint-algorithms/51.md [Latest](https://gromacs.bioexcel.eu/latest.md) · [Categories](https://gromacs.bioexcel.eu/categories.md) · [Tags](https://gromacs.bioexcel.eu/tags.md) --- ## [Question about how LINCS calculates stress](https://gromacs.bioexcel.eu/t/question-about-how-lincs-calculates-stress/13123)
**Author:** [@lynn2](https://gromacs.bioexcel.eu/u/lynn2)\ **Replies:** 5\ **Last updated:** [January 30, 2026, 10:38am UTC](https://gromacs.bioexcel.eu/t/question-about-how-lincs-calculates-stress/13123 "2026-01-30T10:38:39Z")
GROMACS version: 2022.2 GROMACS modification: No Dear Community, I’m using GROMACS to simulate polymers and study the stress relaxation using Green-Kubo relationship. The polymer is merely bead-spring model. I compare… --- ## [Segmentation fault with REMD+GPU--potential bug?](https://gromacs.bioexcel.eu/t/segmentation-fault-with-remd-gpu-potential-bug/11807)
**Author:** [@ianbongalonta](https://gromacs.bioexcel.eu/u/ianbongalonta)\ **Replies:** 5\ **Last updated:** [April 11, 2025, 1:46pm UTC](https://gromacs.bioexcel.eu/t/segmentation-fault-with-remd-gpu-potential-bug/11807 "2025-04-11T13:46:02Z")
GROMACS version: gromacs/2024.1+oneapi-2023.1 GROMACS modification: No Hi everyone, I am currently running a replica exchange simulation on a 30-mer of the PNIPAM polymer, with a modified OPLS-AA and SPCE water (from … --- ## [Gpu update giving error with protein ligand complex](https://gromacs.bioexcel.eu/t/gpu-update-giving-error-with-protein-ligand-complex/5925)
**Author:** [@Adwaith99](https://gromacs.bioexcel.eu/u/Adwaith99)\ **Replies:** 10\ **Last updated:** [December 23, 2024, 11:58am UTC](https://gromacs.bioexcel.eu/t/gpu-update-giving-error-with-protein-ligand-complex/5925 "2024-12-23T11:58:24Z")
GROMACS version: 2022.3 GROMACS modification: No Here post your question: I am doing a simulation of a membrane protein complex with a small molecule ligand. I am running it on a cluster with nodes having four GPUs. I… --- ## [How to solve "Too many LINCS warnings"?](https://gromacs.bioexcel.eu/t/how-to-solve-too-many-lincs-warnings/572)
**Author:** [@Sumedha](https://gromacs.bioexcel.eu/u/Sumedha)\ **Replies:** 4\ **Last updated:** [January 27, 2024, 4:32am UTC](https://gromacs.bioexcel.eu/t/how-to-solve-too-many-lincs-warnings/572 "2024-01-27T04:32:04Z")
GROMACS version: 5.1.2 GROMACS modification: Yes/No Here post your question Hi, I am simulating MraY protein which is a protein found in thermophiles. At the step of NVT i am getting error for “Too many LINCS warnings… --- ## [Should all bonds be constrained in lipid bilayer simulations with CHARMM36?](https://gromacs.bioexcel.eu/t/should-all-bonds-be-constrained-in-lipid-bilayer-simulations-with-charmm36/7070)
**Author:** [@RomanS](https://gromacs.bioexcel.eu/u/RomanS)\ **Replies:** 1\ **Last updated:** [August 23, 2023, 9:27pm UTC](https://gromacs.bioexcel.eu/t/should-all-bonds-be-constrained-in-lipid-bilayer-simulations-with-charmm36/7070 "2023-08-23T21:27:12Z")
GROMACS version: 2023 GROMACS modification: Yes According to the documentation, only h-bonds should be constrained with CHARMM36. Does that apply to simulations of lipid bilayers, or should all bonds be constrained? --- ## [How to put constraints on MARTINI beads](https://gromacs.bioexcel.eu/t/how-to-put-constraints-on-martini-beads/6641)
**Author:** [@SasPanda](https://gromacs.bioexcel.eu/u/SasPanda)\ **Replies:** 0\ **Last updated:** [June 19, 2023, 8:13pm UTC](https://gromacs.bioexcel.eu/t/how-to-put-constraints-on-martini-beads/6641 "2023-06-19T20:13:00Z")
GROMACS version: 2019.6 GROMACS modification: No Here post your question I want to put constraints on a group of SiO2 MARTINI beads forming a shape of a square pyramidal structure (AFM tip structure). Actually, I want… --- ## [NVT grompp warning about constraints](https://gromacs.bioexcel.eu/t/nvt-grompp-warning-about-constraints/5599)
**Author:** [@lalvare](https://gromacs.bioexcel.eu/u/lalvare)\ **Replies:** 0\ **Last updated:** [January 18, 2023, 8:25pm UTC](https://gromacs.bioexcel.eu/t/nvt-grompp-warning-about-constraints/5599 "2023-01-18T20:25:56Z")
GROMACS version:2018 GROMACS modification: NO Hello! I am currently trying to run an MD simulation of 1 small drug molecule with a DOPC lipid bilayer using the united-atom Berger lipid FF. I generated the topology us…