# \#awh **URL:** https://gromacs.bioexcel.eu/tag/awh/35.md [Latest](https://gromacs.bioexcel.eu/latest.md) · [Categories](https://gromacs.bioexcel.eu/categories.md) · [Tags](https://gromacs.bioexcel.eu/tags.md) --- ## [AWH convergence for a charged ligand permeating a bilayer](https://gromacs.bioexcel.eu/t/awh-convergence-for-a-charged-ligand-permeating-a-bilayer/13590)
**Author:** [@Zahraibt7](https://gromacs.bioexcel.eu/u/Zahraibt7)\ **Replies:** 5\ **Last updated:** [July 28, 2026, 5:44am UTC](https://gromacs.bioexcel.eu/t/awh-convergence-for-a-charged-ligand-permeating-a-bilayer/13590 "2026-07-28T05:44:44Z")
GROMACS version: 2023.2-plumed\_2.10.0\_dev GROMACS modification: No Hello everyone, I am applying AWH to study the permeation of a charged ligand (with -2 charge) through a DOPC bilayer. My setup is largely based on th… --- ## [Calculating the free energy of binding using AWH approach](https://gromacs.bioexcel.eu/t/calculating-the-free-energy-of-binding-using-awh-approach/13410)
**Author:** [@lorena.zuzic](https://gromacs.bioexcel.eu/u/lorena.zuzic)\ **Replies:** 8\ **Last updated:** [May 28, 2026, 11:19am UTC](https://gromacs.bioexcel.eu/t/calculating-the-free-energy-of-binding-using-awh-approach/13410 "2026-05-28T11:19:13Z")
GROMACS version: 2026.1 GROMACS modification: No Dear Gromacs community, I am trying to perform binding free energy calculations of a ligand binding to a protein using the AWH method. I am using a general approach des… --- ## [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… --- ## [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… --- ## [Martini AWH: Drug–polymer complex does not permeate membrane with position restraints; complex break](https://gromacs.bioexcel.eu/t/martini-awh-drug-polymer-complex-does-not-permeate-membrane-with-position-restraints-complex-break/13370)
**Author:** [@ubaidmalik3780](https://gromacs.bioexcel.eu/u/ubaidmalik3780)\ **Replies:** 0\ **Last updated:** [April 9, 2026, 6:08am UTC](https://gromacs.bioexcel.eu/t/martini-awh-drug-polymer-complex-does-not-permeate-membrane-with-position-restraints-complex-break/13370 "2026-04-09T06:08:16Z")
GROMACS version: GROMACS modification: Yes/No System description I am performing Martini CG AWH simulations of a drug–polymer complex (BDQ–polymer) interacting with a POPC membrane. Membrane: POPC bilayer Model… --- ## [Awh - gromacs 2026.1](https://gromacs.bioexcel.eu/t/awh-gromacs-2026-1/13335)
**Author:** [@Marius](https://gromacs.bioexcel.eu/u/Marius)\ **Replies:** 7\ **Last updated:** [March 27, 2026, 1:10pm UTC](https://gromacs.bioexcel.eu/t/awh-gromacs-2026-1/13335 "2026-03-27T13:10:58Z")
GROMACS version: 2026.1 GROMACS modification: Yes - Patched with PLUMED/CP2K Hi, I am currently trying to apply the AWH method for a small QM/MM system (two amino acids in water). Unfortunately, I am facing an Asserti… --- ## [AWH with direction-relative | Assertion failed: Condition: weightSum \> 0](https://gromacs.bioexcel.eu/t/awh-with-direction-relative-assertion-failed-condition-weightsum-0/13323)
**Author:** [@hansdewinter](https://gromacs.bioexcel.eu/u/hansdewinter)\ **Replies:** 4\ **Last updated:** [March 25, 2026, 2:49pm UTC](https://gromacs.bioexcel.eu/t/awh-with-direction-relative-assertion-failed-condition-weightsum-0/13323 "2026-03-25T14:49:38Z")
GROMACS version: 2024.3-plumed\_2.9.3 GROMACS modification: Yes/No Hi, we are working on a protein system in which we want to explore the PMF of a ligand moving out of the pocket into the solvent. We want to steer the … --- ## [Accelerated Weight Histogram Method: from Principles to Practice](https://gromacs.bioexcel.eu/t/accelerated-weight-histogram-method-from-principles-to-practice/13206)
**Author:** [@avilla](https://gromacs.bioexcel.eu/u/avilla)\ **Replies:** 0\ **Last updated:** [February 10, 2026, 10:07am UTC](https://gromacs.bioexcel.eu/t/accelerated-weight-histogram-method-from-principles-to-practice/13206 "2026-02-10T10:07:04Z")
Webinar and Tutorial on Accelerated Weight Histogram Method (AWH) Two new tutorials on how to use AWH within the molecular dynamics engine, GROMACS. In the first tutorial, AWH Basic Potential of Mean Force and Converge… --- ## [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… --- ## [Awh friction tensor and friction metric relation with two reaction coordinates](https://gromacs.bioexcel.eu/t/awh-friction-tensor-and-friction-metric-relation-with-two-reaction-coordinates/11890)
**Author:** [@mvuorte](https://gromacs.bioexcel.eu/u/mvuorte)\ **Replies:** 5\ **Last updated:** [December 12, 2025, 4:18pm UTC](https://gromacs.bioexcel.eu/t/awh-friction-tensor-and-friction-metric-relation-with-two-reaction-coordinates/11890 "2025-12-12T16:18:33Z")
Hi, I am trying to understand how the friction metric (last collum in the awh .xvg output file) is calculated from the components of the friction tensor in the optional output file when running awh with two reaction cor… --- ## [Updating diffusion constant midway through the simulation run](https://gromacs.bioexcel.eu/t/updating-diffusion-constant-midway-through-the-simulation-run/13005)
**Author:** [@lorena.zuzic](https://gromacs.bioexcel.eu/u/lorena.zuzic)\ **Replies:** 2\ **Last updated:** [December 5, 2025, 10:09am UTC](https://gromacs.bioexcel.eu/t/updating-diffusion-constant-midway-through-the-simulation-run/13005 "2025-12-05T10:09:26Z")
GROMACS version: 2024 GROMACS modification: No I have been running an AWH simulation for 1 us before realising that the diffusion constant is perhaps too low, due to the lack of convergence. Is it ‘allowed’ to update t… --- ## [AWH multiple .xvg files analysis](https://gromacs.bioexcel.eu/t/awh-multiple-xvg-files-analysis/12134)
**Author:** [@kimiasnn](https://gromacs.bioexcel.eu/u/kimiasnn)\ **Replies:** 1\ **Last updated:** [June 5, 2025, 11:03am UTC](https://gromacs.bioexcel.eu/t/awh-multiple-xvg-files-analysis/12134 "2025-06-05T11:03:17Z")
GROMACS version:gromacs-2023.4 GROMACS modification: Yes Dear All, I ran an accelerated weighted histogram for 100 ns, and I want to analyze my data to calculate the potential of mean force (PMF). However, when I run: … --- ## [AWH Error During Ligand-Membrane Pulling in Z-direction](https://gromacs.bioexcel.eu/t/awh-error-during-ligand-membrane-pulling-in-z-direction/11857)
**Author:** [@bioinfo2025](https://gromacs.bioexcel.eu/u/bioinfo2025)\ **Replies:** 1\ **Last updated:** [April 4, 2025, 8:26am UTC](https://gromacs.bioexcel.eu/t/awh-error-during-ligand-membrane-pulling-in-z-direction/11857 "2025-04-04T08:26:18Z")
GROMACS version: 2025.0 stepX\_pull3.mdp (3.2 KB) GROMACS modification: Yes/No Dear All, While attempting to run an AWH-based pulling simulation, I’m encountering an issue where a compound is biased to move through a … --- ## [Estimating diffusion constant for AWH simulation](https://gromacs.bioexcel.eu/t/estimating-diffusion-constant-for-awh-simulation/11071)
**Author:** [@roozi](https://gromacs.bioexcel.eu/u/roozi)\ **Replies:** 1\ **Last updated:** [January 28, 2025, 11:42am UTC](https://gromacs.bioexcel.eu/t/estimating-diffusion-constant-for-awh-simulation/11071 "2025-01-28T11:42:25Z")
GROMACS version:2024.3 GROMACS modification: No Hi I want to run a protein in water simulation to estimate some PMF using AWH method. As i know, Diffusion constant (D) is a key .mdp file entry to secure a fast and y… --- ## [Analysis of AWH simulations](https://gromacs.bioexcel.eu/t/analysis-of-awh-simulations/10517)
**Author:** [@felippe\_colombari](https://gromacs.bioexcel.eu/u/felippe_colombari)\ **Replies:** 2\ **Last updated:** [November 18, 2024, 5:57pm UTC](https://gromacs.bioexcel.eu/t/analysis-of-awh-simulations/10517 "2024-11-18T17:57:55Z")
GROMACS version: 2024.1 GROMACS modification: Yes/No Dear all, I just learned about the AWH method, and found it very interesting and powerful (I am simulating the binding of small ligands into protein active sites). … --- ## [Advice needed: AWH and Pull code debugging](https://gromacs.bioexcel.eu/t/advice-needed-awh-and-pull-code-debugging/9791)
**Author:** [@Hannah](https://gromacs.bioexcel.eu/u/Hannah)\ **Replies:** 9\ **Last updated:** [September 24, 2024, 8:51am UTC](https://gromacs.bioexcel.eu/t/advice-needed-awh-and-pull-code-debugging/9791 "2024-09-24T08:51:03Z")
GROMACS version: 2023.2 GROMACS modification: No Here post your question Hi, I’m working on pulling a peptide into a lipid bilayer using AWH and the pull code in GROMACS. Below is my complete configuration for the pu… --- ## [AWH Sampling](https://gromacs.bioexcel.eu/t/awh-sampling/10152)
**Author:** [@Erik22](https://gromacs.bioexcel.eu/u/Erik22)\ **Replies:** 2\ **Last updated:** [September 16, 2024, 8:58am UTC](https://gromacs.bioexcel.eu/t/awh-sampling/10152 "2024-09-16T08:58:43Z")
GROMACS version: 2022.4 GROMACS modification: No Hi, I am currently trying to run a AWH multiwalker simulation, using 4 walkers for a single bias, to transition an amino acid side chain from one side to the other. I’v… --- ## [Combined analysis of independent AWH runs](https://gromacs.bioexcel.eu/t/combined-analysis-of-independent-awh-runs/10141)
**Author:** [@ximi](https://gromacs.bioexcel.eu/u/ximi)\ **Replies:** 6\ **Last updated:** [September 11, 2024, 2:32pm UTC](https://gromacs.bioexcel.eu/t/combined-analysis-of-independent-awh-runs/10141 "2024-09-11T14:32:23Z")
GROMACS version: 2022.2 GROMACS modification: No Dear GROMACS forum, I setup two independent runs using AWH with pull code. I simply ran simulations independently, not using -multidir. The two runs have the same setup… --- ## [Multi-walker awh simulation using one gpu](https://gromacs.bioexcel.eu/t/multi-walker-awh-simulation-using-one-gpu/9986)
**Author:** [@roozi](https://gromacs.bioexcel.eu/u/roozi)\ **Replies:** 2\ **Last updated:** [August 27, 2024, 3:58am UTC](https://gromacs.bioexcel.eu/t/multi-walker-awh-simulation-using-one-gpu/9986 "2024-08-27T03:58:38Z")
GROMACS version:2024.2 GROMACS modification: No Hi, I am trying to run a multi-walker awh simulation with 2 walkers and a single bias. I wish to use my pc with one gpu and 32 cores to run it. So to that end, i have co… --- ## [AWH reaction coordinate](https://gromacs.bioexcel.eu/t/awh-reaction-coordinate/2482)
**Author:** [@fabio](https://gromacs.bioexcel.eu/u/fabio)\ **Replies:** 2\ **Last updated:** [February 14, 2024, 12:15pm UTC](https://gromacs.bioexcel.eu/t/awh-reaction-coordinate/2482 "2024-02-14T12:15:18Z")
GROMACS version: 2018 GROMACS modification: No Hi all, I have a protein with two reacting groups. The distance between them observed in the x-ray structure is considered too long for that reaction to occur. So, a move… --- ## [AWH very large free energy barriers](https://gromacs.bioexcel.eu/t/awh-very-large-free-energy-barriers/7832)
**Author:** [@Noob](https://gromacs.bioexcel.eu/u/Noob)\ **Replies:** 13\ **Last updated:** [December 18, 2023, 10:59am UTC](https://gromacs.bioexcel.eu/t/awh-very-large-free-energy-barriers/7832 "2023-12-18T10:59:45Z")
GROMACS version: 2023.3 GROMACS modification: No I have been trying to run a Free energy simulation using AWH and no matter what I set some of the values too I keep getting the same error: ----------------------------… --- ## [How to set awh1-dim1-diffusion and awh1-error-init properly](https://gromacs.bioexcel.eu/t/how-to-set-awh1-dim1-diffusion-and-awh1-error-init-properly/7811)
**Author:** [@Noob](https://gromacs.bioexcel.eu/u/Noob)\ **Replies:** 4\ **Last updated:** [December 12, 2023, 8:34pm UTC](https://gromacs.bioexcel.eu/t/how-to-set-awh1-dim1-diffusion-and-awh1-error-init-properly/7811 "2023-12-12T20:34:37Z")
GROMACS version: 2023.3 GROMACS modification: No I have been trying out the AWH accelerated sampling for gromacs to better sample the conformational space of a protein. I followed the AWH tutorial for gromacs using mor… --- ## [PMF of a small molecule across a slab that has vapor-liquid interface](https://gromacs.bioexcel.eu/t/pmf-of-a-small-molecule-across-a-slab-that-has-vapor-liquid-interface/7046)
**Author:** [@sptiwari](https://gromacs.bioexcel.eu/u/sptiwari)\ **Replies:** 1\ **Last updated:** [August 21, 2023, 6:28am UTC](https://gromacs.bioexcel.eu/t/pmf-of-a-small-molecule-across-a-slab-that-has-vapor-liquid-interface/7046 "2023-08-21T06:28:04Z")
GROMACS version: GROMACS modification: No Dear users, Consider the setup of a simulation box shown in attached image file. Box contains vapor-liquid interface, and consists of water and monoethanolamine (a small molec… --- ## [AWH assertion failed error](https://gromacs.bioexcel.eu/t/awh-assertion-failed-error/6722)
**Author:** [@FelipeRM](https://gromacs.bioexcel.eu/u/FelipeRM)\ **Replies:** 3\ **Last updated:** [July 25, 2023, 10:30am UTC](https://gromacs.bioexcel.eu/t/awh-assertion-failed-error/6722 "2023-07-25T10:30:23Z")
GROMACS version: 2023.1 GROMACS modification: No Hello! I am trying to run an AWH simulation of a DNA/RNA hybrid molecule. My pull groups are two atoms in the backbone of the RNA in adjacent nucleotides, the reaction c… --- ## [AWH and PMF convergence](https://gromacs.bioexcel.eu/t/awh-and-pmf-convergence/5934)
**Author:** [@Gmx\_QA](https://gromacs.bioexcel.eu/u/Gmx_QA)\ **Replies:** 10\ **Last updated:** [March 10, 2023, 7:10pm UTC](https://gromacs.bioexcel.eu/t/awh-and-pmf-convergence/5934 "2023-03-10T19:10:13Z")
GROMACS version: 2022 GROMACS modification: no Hi all, I have been experimenting a little bit with the AWH feature (thanks to the developers) for the purpose of obtaining PMFs for passage of a fairly large molecule (n… --- ## [Transformation pull co-ordinate dihedral maths is odd](https://gromacs.bioexcel.eu/t/transformation-pull-co-ordinate-dihedral-maths-is-odd/5683)
**Author:** [@WillPPK](https://gromacs.bioexcel.eu/u/WillPPK)\ **Replies:** 7\ **Last updated:** [February 1, 2023, 11:44am UTC](https://gromacs.bioexcel.eu/t/transformation-pull-co-ordinate-dihedral-maths-is-odd/5683 "2023-02-01T11:44:26Z")
GROMACS version: 2022.3 GROMACS modification: No I have these transformations pull co-ordinate for dihedral in the mdp file for 4-Ala as a test case. pull-coord5-geometry = transformation pull-coord5-groups … --- ## [Memory issue with 2D AWH and angle](https://gromacs.bioexcel.eu/t/memory-issue-with-2d-awh-and-angle/5538)
**Author:** [@WillPPK](https://gromacs.bioexcel.eu/u/WillPPK)\ **Replies:** 12\ **Last updated:** [January 10, 2023, 1:19pm UTC](https://gromacs.bioexcel.eu/t/memory-issue-with-2d-awh-and-angle/5538 "2023-01-10T13:19:04Z")
GROMACS version: 2022.3, 2022 GROMACS modification: No I ran 2D-AWH on Piz Daint and encounter this error. slurmstepd: error: Detected 1 oom-kill event(s) in StepId=44077037.0 cgroup. Some of your processes may have b… --- ## [AWH Sampling across periodic boundaries](https://gromacs.bioexcel.eu/t/awh-sampling-across-periodic-boundaries/4876)
**Author:** [@himberts](https://gromacs.bioexcel.eu/u/himberts)\ **Replies:** 3\ **Last updated:** [September 28, 2022, 11:38am UTC](https://gromacs.bioexcel.eu/t/awh-sampling-across-periodic-boundaries/4876 "2022-09-28T11:38:33Z")
GROMACS version:2022-03 GROMACS modification: No I am trying to determine the Potential of mean force profile for a ligand passing through a membrane. I was planning to use gromac’s AWH tool. I would like to pull the l… --- ## [Convergence for awh](https://gromacs.bioexcel.eu/t/convergence-for-awh/4266)
**Author:** [@k1797](https://gromacs.bioexcel.eu/u/k1797)\ **Replies:** 3\ **Last updated:** [June 8, 2022, 7:56am UTC](https://gromacs.bioexcel.eu/t/convergence-for-awh/4266 "2022-06-08T07:56:21Z")
GROMACS version:2020 GROMACS modification: No Hello, I am running a multiple walker awh simulation on a 1-D reaction coordinate. Upon comparing the PMFs at different times the PMF is converged. I also checked that the… --- ## [Standard error on AWH free energy estimate?](https://gromacs.bioexcel.eu/t/standard-error-on-awh-free-energy-estimate/4227)
**Author:** [@carruthj](https://gromacs.bioexcel.eu/u/carruthj)\ **Replies:** 6\ **Last updated:** [June 7, 2022, 9:34am UTC](https://gromacs.bioexcel.eu/t/standard-error-on-awh-free-energy-estimate/4227 "2022-06-07T09:34:30Z")
Is it possible to get a standard error associated with a free energy estimate with gmx awh similar to what is given by gmx bar? I tried using gmx bar on the dhdl.xvg file and it just spits out a segmentation fault. [Next page](https://gromacs.bioexcel.eu/tag/awh/35.md?match_all_tags=true&page=1&tags%5B%5D=awh)