# \#mdp-parameters **URL:** https://gromacs.bioexcel.eu/tag/mdp-parameters/6.md [Latest](https://gromacs.bioexcel.eu/latest.md) · [Categories](https://gromacs.bioexcel.eu/categories.md) · [Tags](https://gromacs.bioexcel.eu/tags.md) --- ## [Mdp file differences between CHARMM27 and CHARMM36 parameters](https://gromacs.bioexcel.eu/t/mdp-file-differences-between-charmm27-and-charmm36-parameters/13747)
**Author:** [@ishanipaul](https://gromacs.bioexcel.eu/u/ishanipaul)\ **Replies:** 4\ **Last updated:** [October 7, 2026, 12:01pm UTC](https://gromacs.bioexcel.eu/t/mdp-file-differences-between-charmm27-and-charmm36-parameters/13747 "2026-10-07T12:01:23Z")
GROMACS version: 2024.5 GROMACS modification: No The new version of GROMACS documentation suggests the following modification in the md.mdp file for CHARMM36 forcefield, constraints = h-bonds cutoff-scheme = Verlet … --- ## [PBC Box Failing to Expand to Input .gro File Parameters + Unwanted Position Restrained Protein](https://gromacs.bioexcel.eu/t/pbc-box-failing-to-expand-to-input-gro-file-parameters-unwanted-position-restrained-protein/12152)
**Author:** [@kbwarren](https://gromacs.bioexcel.eu/u/kbwarren)\ **Replies:** 3\ **Last updated:** [September 2, 2026, 7:51pm UTC](https://gromacs.bioexcel.eu/t/pbc-box-failing-to-expand-to-input-gro-file-parameters-unwanted-position-restrained-protein/12152 "2026-09-02T19:51:32Z")
GROMACS version: 2024.4 GROMACS modification: No Hi all, Just posting to this forum because after running a triplicate of coarse-grain lipid bilayer systems with added proteins, I was surprised with very uncharacteris… --- ## [NPγT vs NPT for Unrestrained Membrane Equilibration Using the CHARMM36 Force Field](https://gromacs.bioexcel.eu/t/np-t-vs-npt-for-unrestrained-membrane-equilibration-using-the-charmm36-force-field/13653)
**Author:** [@xlr8](https://gromacs.bioexcel.eu/u/xlr8)\ **Replies:** 10\ **Last updated:** [August 26, 2026, 2:43pm UTC](https://gromacs.bioexcel.eu/t/np-t-vs-npt-for-unrestrained-membrane-equilibration-using-the-charmm36-force-field/13653 "2026-08-26T14:43:44Z")
GROMACS version:2025 GROMACS modification: Yes/No Here post your question Hello everyone, I am currently setting up a membrane protein simulation using the CHARMM36m force field and would appreciate some guidance reg… --- ## [CUDA illegal memory access during NPT equilibration](https://gromacs.bioexcel.eu/t/cuda-illegal-memory-access-during-npt-equilibration/13673)
**Author:** [@shreyasd2](https://gromacs.bioexcel.eu/u/shreyasd2)\ **Replies:** 9\ **Last updated:** [August 21, 2026, 4:08pm UTC](https://gromacs.bioexcel.eu/t/cuda-illegal-memory-access-during-npt-equilibration/13673 "2026-08-21T16:08:51Z")
GROMACS version: 2026.0 GROMACS modification: No Dear all, I am simulating a highly dense system containing carbohydrates and amino acids. I am performing a multistep equilibration protocol with gradually decreasing f… --- ## [C-rescale barostat and simulated annealing](https://gromacs.bioexcel.eu/t/c-rescale-barostat-and-simulated-annealing/13652)
**Author:** [@Marius](https://gromacs.bioexcel.eu/u/Marius)\ **Replies:** 4\ **Last updated:** [August 6, 2026, 2:48pm UTC](https://gromacs.bioexcel.eu/t/c-rescale-barostat-and-simulated-annealing/13652 "2026-08-06T14:48:24Z")
GROMACS version: 2025.4 / 2021 GROMACS modification: 2025.4 (No) / 2021 (Yes) Hi, I recently stumbled across an issue running grompp for a simulation using simulated annealing. For temperature coupling I am using the … --- ## [Z‑dimension of the box decreases](https://gromacs.bioexcel.eu/t/z-dimension-of-the-box-decreases/13631)
**Author:** [@ZXY](https://gromacs.bioexcel.eu/u/ZXY)\ **Replies:** 3\ **Last updated:** [August 5, 2026, 10:09am UTC](https://gromacs.bioexcel.eu/t/z-dimension-of-the-box-decreases/13631 "2026-08-05T10:09:26Z")
GROMACS version:2018 GROMACS modification: Yes/No Here post your question “Dear all, I am using the Martini 3‑IDP force field to simulate a system consisting of a spherical protein condensate and a cell membrane (DIPC… --- ## [Trans to cis confirmation at NVT step](https://gromacs.bioexcel.eu/t/trans-to-cis-confirmation-at-nvt-step/13623)
**Author:** [@RUTUJITA](https://gromacs.bioexcel.eu/u/RUTUJITA)\ **Replies:** 0\ **Last updated:** [July 28, 2026, 5:27am UTC](https://gromacs.bioexcel.eu/t/trans-to-cis-confirmation-at-nvt-step/13623 "2026-07-28T05:27:12Z")
GROMACS version: 2025.4 GROMACS modification: Yes/No I am working with Chalcones as ligand with protein. Initially these chalcones are in trans confirmation. One of the chalcone derivative becomes cis after NVT step. F… --- ## [How many nanoseconds do I need to capture potential unbinding events for protein-protein interaction](https://gromacs.bioexcel.eu/t/how-many-nanoseconds-do-i-need-to-capture-potential-unbinding-events-for-protein-protein-interaction/13572)
**Author:** [@Kael](https://gromacs.bioexcel.eu/u/Kael)\ **Replies:** 1\ **Last updated:** [July 4, 2026, 3:10pm UTC](https://gromacs.bioexcel.eu/t/how-many-nanoseconds-do-i-need-to-capture-potential-unbinding-events-for-protein-protein-interaction/13572 "2026-07-04T15:10:40Z")
GROMACS version: 2026.1 GROMACS modification: No Hi! I’m currently performing MD analysis of receptor-cytokine interaction (ppi) within 200 nanoseconds. I’m testing single-point mutation on cytokines, and I want to ca… --- ## [Deform by Gromacs to apply shear rate](https://gromacs.bioexcel.eu/t/deform-by-gromacs-to-apply-shear-rate/1962)
**Author:** [@MOH4](https://gromacs.bioexcel.eu/u/MOH4)\ **Replies:** 8\ **Last updated:** [June 9, 2026, 6:34am UTC](https://gromacs.bioexcel.eu/t/deform-by-gromacs-to-apply-shear-rate/1962 "2026-06-09T06:34:38Z")
Dear all, I mean to use deform for applying shear rate on my system, but, I could not find any tutorials on this regard. Could you please tell me how I can do deform by gromacs (step by step please)? And, How can I un… --- ## [COM motion removal during NVT simulation with electric field](https://gromacs.bioexcel.eu/t/com-motion-removal-during-nvt-simulation-with-electric-field/13447)
**Author:** [@Afi](https://gromacs.bioexcel.eu/u/Afi)\ **Replies:** 5\ **Last updated:** [May 19, 2026, 6:18am UTC](https://gromacs.bioexcel.eu/t/com-motion-removal-during-nvt-simulation-with-electric-field/13447 "2026-05-19T06:18:22Z")
Hi, I am studying the motion of a positively charged protein in the presence of electric field at 300 K. I have observed a conflict between maintaining the physical drift of the protein under the influence of electric f… --- ## [Mdrun with awh for a dimeric protein](https://gromacs.bioexcel.eu/t/mdrun-with-awh-for-a-dimeric-protein/13428)
**Author:** [@csnail](https://gromacs.bioexcel.eu/u/csnail)\ **Replies:** 0\ **Last updated:** [April 29, 2026, 11:35am UTC](https://gromacs.bioexcel.eu/t/mdrun-with-awh-for-a-dimeric-protein/13428 "2026-04-29T11:35:40Z")
GROMACS version: 2025.3 GROMACS modification: No, just the MPI library. I’m currently researching the dimerization of a fragment of zinc-finger protein (calculations are made for two coupled identical chains of 68 amin… --- ## [GROMACS SMD for TCR–pMHC: should TCR be pull group 1 or 2](https://gromacs.bioexcel.eu/t/gromacs-smd-for-tcr-pmhc-should-tcr-be-pull-group-1-or-2/13414)
**Author:** [@rachana](https://gromacs.bioexcel.eu/u/rachana)\ **Replies:** 0\ **Last updated:** [April 25, 2026, 10:04pm UTC](https://gromacs.bioexcel.eu/t/gromacs-smd-for-tcr-pmhc-should-tcr-be-pull-group-1-or-2/13414 "2026-04-25T22:04:25Z")
GROMACS version: GROMACS modification: Yes/No Here post your question I am setting up constant-velocity SMD for a TCR–pMHC system. The C-terminal Cα of the MHC α-chain is position-restrained as the anchor, and the pul… --- ## [Using AWH for bilayer permeability](https://gromacs.bioexcel.eu/t/using-awh-for-bilayer-permeability/6727)
**Author:** [@tyd](https://gromacs.bioexcel.eu/u/tyd)\ **Replies:** 18\ **Last updated:** [April 22, 2026, 7:28am UTC](https://gromacs.bioexcel.eu/t/using-awh-for-bilayer-permeability/6727 "2026-04-22T07:28:36Z")
GROMACS version: 2023 GROMACS modification: No Hi! I’m attempting to pull a ribose molecule through a lipid bilayer using AWH and pull-code. I’ve run this system for 600ns without seeing any sampling of the bilayer co… --- ## [Changes of default \`nstpcouple\` and \`nsttcouple\` from version 2022 to 2023](https://gromacs.bioexcel.eu/t/changes-of-default-nstpcouple-and-nsttcouple-from-version-2022-to-2023/6220)
**Author:** [@Valentina](https://gromacs.bioexcel.eu/u/Valentina)\ **Replies:** 35\ **Last updated:** [April 14, 2026, 7:41am UTC](https://gromacs.bioexcel.eu/t/changes-of-default-nstpcouple-and-nsttcouple-from-version-2022-to-2023/6220 "2026-04-14T07:41:51Z")
GROMACS version: 2023 GROMACS modification: No Dear all, This is not a question, just something I thought may be worth posting for information. The new 2023 Gromacs made a change in the default nstpcouple and nsttco… --- ## [C-rescale vs Parrinello–Rahman in final NPT equilibration before protein–protein SMD (TCR–pMHC, ~1M](https://gromacs.bioexcel.eu/t/c-rescale-vs-parrinello-rahman-in-final-npt-equilibration-before-protein-protein-smd-tcr-pmhc-1m/13367)
**Author:** [@rachana](https://gromacs.bioexcel.eu/u/rachana)\ **Replies:** 1\ **Last updated:** [April 8, 2026, 7:01am UTC](https://gromacs.bioexcel.eu/t/c-rescale-vs-parrinello-rahman-in-final-npt-equilibration-before-protein-protein-smd-tcr-pmhc-1m/13367 "2026-04-08T07:01:40Z")
GROMACS version: GROMACS modification: Yes/No Here post your question Hi everyone, I’m running GROMACS simulations for a protein–protein system (TCR–pMHC complex) and planning to perform steered MD (SMD) after equili… --- ## [Abnormal dVremain/dl values in GROMACS 2025.0 with vdw-type=pme and free-energy](https://gromacs.bioexcel.eu/t/abnormal-dvremain-dl-values-in-gromacs-2025-0-with-vdw-type-pme-and-free-energy/13344)
**Author:** [@donghwanz](https://gromacs.bioexcel.eu/u/donghwanz)\ **Replies:** 3\ **Last updated:** [March 31, 2026, 6:39am UTC](https://gromacs.bioexcel.eu/t/abnormal-dvremain-dl-values-in-gromacs-2025-0-with-vdw-type-pme-and-free-energy/13344 "2026-03-31T06:39:16Z")
GROMACS version: 2025.0 (bug) / 2024.4 (normal) GROMACS modification: No I found a potential bug in GROMACS 2025.0 related to free energy calculations with LJ-PME (vdw-type=pme). Symptom: GROMACS 2024.4: dVremain/d… --- ## [Coulomb (SR) calculation in PME](https://gromacs.bioexcel.eu/t/coulomb-sr-calculation-in-pme/13301)
**Author:** [@shaunak](https://gromacs.bioexcel.eu/u/shaunak)\ **Replies:** 9\ **Last updated:** [March 19, 2026, 4:23pm UTC](https://gromacs.bioexcel.eu/t/coulomb-sr-calculation-in-pme/13301 "2026-03-19T16:23:31Z")
Hi, I’m trying to understand the calculation of Coulomb (SR) in an alanine dipeptide molecule. In my effort to do so, I read documentation and came across this statement ( Long Range Electrostatics - GROMACS 2026.1 docu… --- ## [Steered Molecular dynamics of a ligand moving towards bilayer membrane](https://gromacs.bioexcel.eu/t/steered-molecular-dynamics-of-a-ligand-moving-towards-bilayer-membrane/13288)
**Author:** [@Ranbir720](https://gromacs.bioexcel.eu/u/Ranbir720)\ **Replies:** 1\ **Last updated:** [March 16, 2026, 9:59am UTC](https://gromacs.bioexcel.eu/t/steered-molecular-dynamics-of-a-ligand-moving-towards-bilayer-membrane/13288 "2026-03-16T09:59:31Z")
GROMACS version: 2025.3 GROMACS modification: No ; Pull code pull = yes pull\_ncoords = 1 ; only one reaction coordinate pull\_ngroups = 2 ; two groups defining… --- ## [Paradoxical Density in OPLS-AA: Diesel mixture density is abnormally LOWER than its lightest compone](https://gromacs.bioexcel.eu/t/paradoxical-density-in-opls-aa-diesel-mixture-density-is-abnormally-lower-than-its-lightest-compone/13303)
**Author:** [@scorpion1028](https://gromacs.bioexcel.eu/u/scorpion1028)\ **Replies:** 6\ **Last updated:** [March 15, 2026, 4:58am UTC](https://gromacs.bioexcel.eu/t/paradoxical-density-in-opls-aa-diesel-mixture-density-is-abnormally-lower-than-its-lightest-compone/13303 "2026-03-15T04:58:54Z")
GROMACS version:2022.03 GROMACS modification: Yes/No Here post your question Dear GROMACS Community, I am currently working on simulating a complex diesel surrogate fuel system (a mixture of various hydrocarbons rang… --- ## [Hydrogen mass repartitioning + multiple time step](https://gromacs.bioexcel.eu/t/hydrogen-mass-repartitioning-multiple-time-step/13246)
**Author:** [@ncheron](https://gromacs.bioexcel.eu/u/ncheron)\ **Replies:** 2\ **Last updated:** [March 7, 2026, 11:58am UTC](https://gromacs.bioexcel.eu/t/hydrogen-mass-repartitioning-multiple-time-step/13246 "2026-03-07T11:58:45Z")
GROMACS version: 2024 or higher GROMACS modification: No Hi, I am a little bit confused by the recommandations provided here: Getting good performance from mdrun - GROMACS 2026.0 documentation . If I set mass-repartit… --- ## [ERROR 1 rvdw-switch must be \< rvdw INQUIRY?](https://gromacs.bioexcel.eu/t/error-1-rvdw-switch-must-be-rvdw-inquiry/13282)
**Author:** [@mjsubach](https://gromacs.bioexcel.eu/u/mjsubach)\ **Replies:** 4\ **Last updated:** [March 5, 2026, 8:44pm UTC](https://gromacs.bioexcel.eu/t/error-1-rvdw-switch-must-be-rvdw-inquiry/13282 "2026-03-05T20:44:05Z")
GROMACS version: 2025.3 GROMACS modification: Yes/No Here post your question: Hello I CHARMM\_GUI generated a gromacs step6.0\_minimization.mdp file for a large transmembrane-ligand complex, the below error/notes were … --- ## [Steered MD Simulation error](https://gromacs.bioexcel.eu/t/steered-md-simulation-error/13144)
**Author:** [@Aneesha.A](https://gromacs.bioexcel.eu/u/Aneesha.A)\ **Replies:** 19\ **Last updated:** [February 19, 2026, 3:24pm UTC](https://gromacs.bioexcel.eu/t/steered-md-simulation-error/13144 "2026-02-19T15:24:06Z")
GROMACS version: 2021.4/gpuvolta GROMACS modification: No Hi everyone, I am following Tutorial 3: Umbrella Sampling, but altering the .mdp files to a method section from a paper (unfortunately the authors are not much… --- ## [Discrete "Coulp.-recip" values for different conformations of the same system](https://gromacs.bioexcel.eu/t/discrete-coulp-recip-values-for-different-conformations-of-the-same-system/13111)
**Author:** [@evli](https://gromacs.bioexcel.eu/u/evli)\ **Replies:** 10\ **Last updated:** [February 18, 2026, 9:25am UTC](https://gromacs.bioexcel.eu/t/discrete-coulp-recip-values-for-different-conformations-of-the-same-system/13111 "2026-02-18T09:25:11Z")
GROMACS version: 2023.2 GROMACS modification: No Hello everyone, I calculated the average energy terms for XG in water across 25 different conformations. All systems are identical, sharing the same water molecules; th… --- ## [Equilibration not work](https://gromacs.bioexcel.eu/t/equilibration-not-work/13223)
**Author:** [@gluizcar](https://gromacs.bioexcel.eu/u/gluizcar)\ **Replies:** 0\ **Last updated:** [February 17, 2026, 1:52pm UTC](https://gromacs.bioexcel.eu/t/equilibration-not-work/13223 "2026-02-17T13:52:46Z")
GROMACS version: 2022 GROMACS modification: NoHi every one. I have this system, jannus MoSSe, with nanopore passivated with H atoms. I generated my force field files via acpype. I tried, many times, to simulation my s… --- ## [SMD simulation - protein pulling and resulting rotation](https://gromacs.bioexcel.eu/t/smd-simulation-protein-pulling-and-resulting-rotation/13181)
**Author:** [@enthusiast](https://gromacs.bioexcel.eu/u/enthusiast)\ **Replies:** 2\ **Last updated:** [February 10, 2026, 9:04am UTC](https://gromacs.bioexcel.eu/t/smd-simulation-protein-pulling-and-resulting-rotation/13181 "2026-02-10T09:04:54Z")
GROMACS version: 2025.2 GROMACS modification: Yes Hello everyone, I am having some questions about my pull code. The idea is to hold a protein via two springs on the two terminals and to pull one terminal along the x… --- ## [Questions regarding AWH and comparison to MBAR](https://gromacs.bioexcel.eu/t/questions-regarding-awh-and-comparison-to-mbar/13180)
**Author:** [@luedsch](https://gromacs.bioexcel.eu/u/luedsch)\ **Replies:** 3\ **Last updated:** [February 10, 2026, 8:11am UTC](https://gromacs.bioexcel.eu/t/questions-regarding-awh-and-comparison-to-mbar/13180 "2026-02-10T08:11:45Z")
GROMACS version: 2025.4 GROMACS modification: No Hello fellow researchers, I am currently figuring out wheatear the implemented AWH method is suited for the efficient calculation of the solvation free energy (SFE) sim… --- ## [\[Errors\] Problems during Umbrella Sampling](https://gromacs.bioexcel.eu/t/errors-problems-during-umbrella-sampling/13169)
**Author:** [@grahzdan](https://gromacs.bioexcel.eu/u/grahzdan)\ **Replies:** 1\ **Last updated:** [February 4, 2026, 9:08am UTC](https://gromacs.bioexcel.eu/t/errors-problems-during-umbrella-sampling/13169 "2026-02-04T09:08:49Z")
GROMACS version: 2022.3-plumed\_2.8.1 GROMACS modification: Yes/No Hi all, I am having an assignment to do simple Umbrella Sampling simulation to calculate Free energy profile for martinized (Martini 3) small peptide a… --- ## [Your Review on AMBER19sb MD in GROMACS2026](https://gromacs.bioexcel.eu/t/your-review-on-amber19sb-md-in-gromacs2026/13167)
**Author:** [@pk1997](https://gromacs.bioexcel.eu/u/pk1997)\ **Replies:** 1\ **Last updated:** [February 4, 2026, 9:05am UTC](https://gromacs.bioexcel.eu/t/your-review-on-amber19sb-md-in-gromacs2026/13167 "2026-02-04T09:05:03Z")
GROMACS version: 2026 GROMACS modification: No Hi, has anyone tried simulating with the newly ported AMBER19SB forcefield in GROMACS 2026? Apart from choosing OPC water model in pdb2gmx selection and ‘gmx solvate -cs … --- ## [The contradiction between the mdp settings and the real pull rate](https://gromacs.bioexcel.eu/t/the-contradiction-between-the-mdp-settings-and-the-real-pull-rate/13161)
**Author:** [@Riggs](https://gromacs.bioexcel.eu/u/Riggs)\ **Replies:** 13\ **Last updated:** [February 4, 2026, 9:02am UTC](https://gromacs.bioexcel.eu/t/the-contradiction-between-the-mdp-settings-and-the-real-pull-rate/13161 "2026-02-04T09:02:22Z")
GROMACS version: 2024.06 GROMACS modification: Yes/No Hello, everyone! I have conduct a simulation of pulling a protein in the specific direction, and my pull seeting of mdp file is as below. But after a short time of … --- ## [Simulated annealing of protein-DNA complex](https://gromacs.bioexcel.eu/t/simulated-annealing-of-protein-dna-complex/13173)
**Author:** [@Maike\_Bublitz](https://gromacs.bioexcel.eu/u/Maike_Bublitz)\ **Replies:** 0\ **Last updated:** [February 3, 2026, 3:42pm UTC](https://gromacs.bioexcel.eu/t/simulated-annealing-of-protein-dna-complex/13173 "2026-02-03T15:42:30Z")
GROMACS version: 2024.2 GROMACS modification: No Dear all, I am trying to set up an atomistic simulation system containing a protein bound to a 19-base stretch of double-stranded DNA. The protein contains 3 zinc-finge… [Next page](https://gromacs.bioexcel.eu/tag/mdp-parameters/6.md?match_all_tags=true&page=1&tags%5B%5D=mdp-parameters)