# \#pull-code **URL:** https://gromacs.bioexcel.eu/tag/pull-code/45.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… --- ## [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… --- ## [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 … --- ## [\[umbrella sampling\] Can I use "pull\_coord1\_geometry = direction" for complexes with cyclodextrins?](https://gromacs.bioexcel.eu/t/umbrella-sampling-can-i-use-pull-coord1-geometry-direction-for-complexes-with-cyclodextrins/13278)
**Author:** [@DariuszKamil](https://gromacs.bioexcel.eu/u/DariuszKamil)\ **Replies:** 1\ **Last updated:** [March 9, 2026, 2:02pm UTC](https://gromacs.bioexcel.eu/t/umbrella-sampling-can-i-use-pull-coord1-geometry-direction-for-complexes-with-cyclodextrins/13278 "2026-03-09T14:02:35Z")
GROMACS version: 2025.3 GROMACS modification: No I would like to kindly ask whether the below described approach is valid from the thermodnamical point of view. Cyclodextrins (CD) are cyclic ologosaccharides, composed… --- ## [Pull code (umbrella, distance): Fatal error "Pull reference distance … needs to be non-negative"](https://gromacs.bioexcel.eu/t/pull-code-umbrella-distance-fatal-error-pull-reference-distance-needs-to-be-non-negative/13207)
**Author:** [@david1](https://gromacs.bioexcel.eu/u/david1)\ **Replies:** 1\ **Last updated:** [February 11, 2026, 8:27am UTC](https://gromacs.bioexcel.eu/t/pull-code-umbrella-distance-fatal-error-pull-reference-distance-needs-to-be-non-negative/13207 "2026-02-11T08:27:39Z")
GROMACS version: 2025.1 GROMACS modification: No I’m using the pull option in GROMACS to bring together two backbone portions (see image below). I monitored the distance between the centers of mass (COM) of both backbo… --- ## [PMF for angle rotations](https://gromacs.bioexcel.eu/t/pmf-for-angle-rotations/1842)
**Author:** [@dr\_m\_ganj](https://gromacs.bioexcel.eu/u/dr_m_ganj)\ **Replies:** 2\ **Last updated:** [December 19, 2025, 6:54pm UTC](https://gromacs.bioexcel.eu/t/pmf-for-angle-rotations/1842 "2025-12-19T18:54:55Z")
GROMACS version: 2018.8 GROMACS modification: Yes/No Dear Justin, I want to evaluate a PMF using umbrella sampling for rotating an atom around a dihedral angle. For example; C1, C2, C3, C4 atoms constructed a dihedral… --- ## [Pull code on a long filament](https://gromacs.bioexcel.eu/t/pull-code-on-a-long-filament/12458)
**Author:** [@Adwaith99](https://gromacs.bioexcel.eu/u/Adwaith99)\ **Replies:** 7\ **Last updated:** [August 12, 2025, 8:51am UTC](https://gromacs.bioexcel.eu/t/pull-code-on-a-long-filament/12458 "2025-08-12T08:51:40Z")
GROMACS version:2024.4 GROMACS modification: No I am trying to run a pulling simulation on a long filament protein. I am using GROMACS pull code for this. The filament is about ~27 nm long. I set up a few residues on e… --- ## [Osmotic pressure simulations using the pull code](https://gromacs.bioexcel.eu/t/osmotic-pressure-simulations-using-the-pull-code/12380)
**Author:** [@cheesecake](https://gromacs.bioexcel.eu/u/cheesecake)\ **Replies:** 6\ **Last updated:** [August 7, 2025, 9:32am UTC](https://gromacs.bioexcel.eu/t/osmotic-pressure-simulations-using-the-pull-code/12380 "2025-08-07T09:32:24Z")
GROMACS version: 2023.2 GROMACS modification: No Hello fellow md simulators, I am trying to do osmotic pressure simulations using gromacs’ pull code as suggested here: gromacs\_mailing\_list I have figured out a way t… --- ## [Query about pullf.xvg plot](https://gromacs.bioexcel.eu/t/query-about-pullf-xvg-plot/12423)
**Author:** [@pratyush](https://gromacs.bioexcel.eu/u/pratyush)\ **Replies:** 4\ **Last updated:** [July 23, 2025, 9:54pm UTC](https://gromacs.bioexcel.eu/t/query-about-pullf-xvg-plot/12423 "2025-07-23T21:54:25Z")
GROMACS version: 2024.2 GROMACS modification: Yes Based on the pull code below, I’m trying to determine whether the resulting force profile is physically reasonable. The force increases steadily in the first 800 ps, sh… --- ## [Pulling simulations help](https://gromacs.bioexcel.eu/t/pulling-simulations-help/12252)
**Author:** [@ghostpipierfish](https://gromacs.bioexcel.eu/u/ghostpipierfish)\ **Replies:** 1\ **Last updated:** [June 28, 2025, 4:50am UTC](https://gromacs.bioexcel.eu/t/pulling-simulations-help/12252 "2025-06-28T04:50:03Z")
GROMACS version: 2019.3/intel-2018 GROMACS modification: No Hi, I’m trying to do a simple pulling simulation in the z direction. I’ve decided to put a position restraint on the N terminus of my protein (the entire fir… --- ## [Simple Pulling script 1D 1 group](https://gromacs.bioexcel.eu/t/simple-pulling-script-1d-1-group/12100)
**Author:** [@lazzari26](https://gromacs.bioexcel.eu/u/lazzari26)\ **Replies:** 0\ **Last updated:** [May 17, 2025, 10:35am UTC](https://gromacs.bioexcel.eu/t/simple-pulling-script-1d-1-group/12100 "2025-05-17T10:35:06Z")
I always struggled in finding a good algorithm for pulling in GROMACS, the tool is good but the documentation is awful. Here I’m just sharing a good script that work for pulling in 1 dimension (x-axis), with a constant … --- ## [LINCS error while performing pull simulations?](https://gromacs.bioexcel.eu/t/lincs-error-while-performing-pull-simulations/11515)
**Author:** [@vardhan](https://gromacs.bioexcel.eu/u/vardhan)\ **Replies:** 17\ **Last updated:** [March 18, 2025, 12:59pm UTC](https://gromacs.bioexcel.eu/t/lincs-error-while-performing-pull-simulations/11515 "2025-03-18T12:59:58Z")
GROMACS version: 2023 GROMACS modification: No I am trying to calculate the PMF of a molecule through a lipid bilayer. I have an equilibrated bilayer. I inserted my molecule of interest (single molecule) using ‘inser… --- ## [Unfolding a 574 aa protein](https://gromacs.bioexcel.eu/t/unfolding-a-574-aa-protein/11442)
**Author:** [@Bharat123](https://gromacs.bioexcel.eu/u/Bharat123)\ **Replies:** 0\ **Last updated:** [February 3, 2025, 12:06pm UTC](https://gromacs.bioexcel.eu/t/unfolding-a-574-aa-protein/11442 "2025-02-03T12:06:30Z")
GROMACS version: 2022.6 GROMACS modification: Yes/No Hello everyone, I am relatively new to gromacs and just learning about Molecular dynamics. I am trying to unfold a mutant and wild-type version of a protein(~574 aa… --- ## [Simultaneous Pulling of Multiple Protein Segments to Different Target Distances in GROMACS](https://gromacs.bioexcel.eu/t/simultaneous-pulling-of-multiple-protein-segments-to-different-target-distances-in-gromacs/10470)
**Author:** [@com\_gro](https://gromacs.bioexcel.eu/u/com_gro)\ **Replies:** 4\ **Last updated:** [December 2, 2024, 6:47am UTC](https://gromacs.bioexcel.eu/t/simultaneous-pulling-of-multiple-protein-segments-to-different-target-distances-in-gromacs/10470 "2024-12-02T06:47:52Z")
Hello, I’m interested in pulling multiple parts of a protein to different distances within a simulation. Is it possible to pull each part simultaneously but to different target distances? For example: Pull part1 to 4… --- ## [Pull-force error](https://gromacs.bioexcel.eu/t/pull-force-error/10556)
**Author:** [@pratyush](https://gromacs.bioexcel.eu/u/pratyush)\ **Replies:** 5\ **Last updated:** [November 15, 2024, 8:09am UTC](https://gromacs.bioexcel.eu/t/pull-force-error/10556 "2024-11-15T08:09:12Z")
GROMACS version: 2022 GROMACS modification: Yes/No So I am doing pull-force calculation of a protein-protein complex where I have to pull the smaller protein from the larger subunit. The pullf.xvg curve seems fine to a… --- ## [Gromacs umbrella sampling error for pull force calculation](https://gromacs.bioexcel.eu/t/gromacs-umbrella-sampling-error-for-pull-force-calculation/10453)
**Author:** [@pratyush](https://gromacs.bioexcel.eu/u/pratyush)\ **Replies:** 4\ **Last updated:** [October 30, 2024, 1:31pm UTC](https://gromacs.bioexcel.eu/t/gromacs-umbrella-sampling-error-for-pull-force-calculation/10453 "2024-10-30T13:31:53Z")
GROMACS version: 2022 GROMACS modification: Yes/No So I guess this will be silly question but I am very much clueless, so please help me out. I have a system where the ligand is complexed with the dimer at their in… --- ## [Rate and force unit conversion for pulling paramters](https://gromacs.bioexcel.eu/t/rate-and-force-unit-conversion-for-pulling-paramters/10271)
**Author:** [@com\_gro](https://gromacs.bioexcel.eu/u/com_gro)\ **Replies:** 1\ **Last updated:** [October 2, 2024, 6:13am UTC](https://gromacs.bioexcel.eu/t/rate-and-force-unit-conversion-for-pulling-paramters/10271 "2024-10-02T06:13:21Z")
Hello good people, I need your help! I know this is very basic, but I want to cross-check if my unit conversions are correct, as I need to use these values for the following two parameters in my simulation. I want to p… --- ## [How to understand the output after pulling force is applied?](https://gromacs.bioexcel.eu/t/how-to-understand-the-output-after-pulling-force-is-applied/10146)
**Author:** [@liuwq](https://gromacs.bioexcel.eu/u/liuwq)\ **Replies:** 11\ **Last updated:** [September 20, 2024, 1:28pm UTC](https://gromacs.bioexcel.eu/t/how-to-understand-the-output-after-pulling-force-is-applied/10146 "2024-09-20T13:28:38Z")
GROMACS version: 2018.8 GROMACS modification: No I have a molecule with a long chain in a simulation box. First, the system is run under NVT condition and the molecule chain will shrink or collapse to a more compact co… --- ## [How to apply constant pull force at two ends of a molecule?](https://gromacs.bioexcel.eu/t/how-to-apply-constant-pull-force-at-two-ends-of-a-molecule/10056)
**Author:** [@liuwq](https://gromacs.bioexcel.eu/u/liuwq)\ **Replies:** 2\ **Last updated:** [September 10, 2024, 6:58am UTC](https://gromacs.bioexcel.eu/t/how-to-apply-constant-pull-force-at-two-ends-of-a-molecule/10056 "2024-09-10T06:58:25Z")
GROMACS version: 2018.8 GROMACS modification: No I have a molecule, and I need to apply pulling forces with opposite directions to a head atom and a tail atom to stretch the molecule to an almost straight configuration… --- ## [Pull code for a single window](https://gromacs.bioexcel.eu/t/pull-code-for-a-single-window/9958)
**Author:** [@arthurmluz](https://gromacs.bioexcel.eu/u/arthurmluz)\ **Replies:** 3\ **Last updated:** [August 22, 2024, 2:48pm UTC](https://gromacs.bioexcel.eu/t/pull-code-for-a-single-window/9958 "2024-08-22T14:48:40Z")
GROMACS version: 2022.2 GROMACS modification: No Hello, everyone! I need to evaluate the free energy contribution of maintaining a molecule within a fixed distance from the center of mass of a phase. I did this by usi… --- ## [Soft/Stiff Spring](https://gromacs.bioexcel.eu/t/soft-stiff-spring/9916)
**Author:** [@ElectricallyCharged](https://gromacs.bioexcel.eu/u/ElectricallyCharged)\ **Replies:** 1\ **Last updated:** [August 19, 2024, 9:53am UTC](https://gromacs.bioexcel.eu/t/soft-stiff-spring/9916 "2024-08-19T09:53:14Z")
GROMACS version: 2024 GROMACS modification: Yes Hi, what is the difference between a stiff spring and a soft spring in steered molecular dynamics. What are the contexts where one should be chosen over the other. Than… --- ## [Free energy calculation with fixed relative position](https://gromacs.bioexcel.eu/t/free-energy-calculation-with-fixed-relative-position/9852)
**Author:** [@arthurmluz](https://gromacs.bioexcel.eu/u/arthurmluz)\ **Replies:** 2\ **Last updated:** [August 12, 2024, 12:15pm UTC](https://gromacs.bioexcel.eu/t/free-energy-calculation-with-fixed-relative-position/9852 "2024-08-12T12:15:48Z")
GROMACS version: 2024/1 GROMACS modification: No Hello everyone! I need to do an alchemical solvation calculation of a molecule. However, I also need to keep the relative position of the coupled molecule and the cente… --- ## [Question about absolute reference point/warning for pulling a protein between solvents](https://gromacs.bioexcel.eu/t/question-about-absolute-reference-point-warning-for-pulling-a-protein-between-solvents/9648)
**Author:** [@NHolditch](https://gromacs.bioexcel.eu/u/NHolditch)\ **Replies:** 0\ **Last updated:** [July 14, 2024, 9:13pm UTC](https://gromacs.bioexcel.eu/t/question-about-absolute-reference-point-warning-for-pulling-a-protein-between-solvents/9648 "2024-07-14T21:13:16Z")
GROMACS version: 2023.2 GROMACS modification: No I am trying to measure the change in free energy of a protein between two solvents, water and a silicon based oil. The system is equilibrated with the protein initially … --- ## [Another Problem with Distances Between Pull Groups](https://gromacs.bioexcel.eu/t/another-problem-with-distances-between-pull-groups/6172)
**Author:** [@kzinga](https://gromacs.bioexcel.eu/u/kzinga)\ **Replies:** 3\ **Last updated:** [July 14, 2024, 10:36am UTC](https://gromacs.bioexcel.eu/t/another-problem-with-distances-between-pull-groups/6172 "2024-07-14T10:36:09Z")
GROMACS version: 2021.3 GROMACS modification: No Hi all, I am attempting to tether multiple proteins to a lipid bilayer using the following pull code: ; Pull Code pull = yes pull-print-com = yes pull\_ngroups = 32 … --- ## [Issues with Pulling Protein Through a Pore: High Forces and Restraint Effects](https://gromacs.bioexcel.eu/t/issues-with-pulling-protein-through-a-pore-high-forces-and-restraint-effects/9407)
**Author:** [@com\_gro](https://gromacs.bioexcel.eu/u/com_gro)\ **Replies:** 2\ **Last updated:** [July 11, 2024, 3:24pm UTC](https://gromacs.bioexcel.eu/t/issues-with-pulling-protein-through-a-pore-high-forces-and-restraint-effects/9407 "2024-07-11T15:24:26Z")
Hello GROMACS community, I am conducting a pulling simulation where one protein is being pulled through the pore of another protein. I have encountered several issues related to the forces experienced by the pulled prot… --- ## [COM pulling of large groups:](https://gromacs.bioexcel.eu/t/com-pulling-of-large-groups/9061)
**Author:** [@kosmith](https://gromacs.bioexcel.eu/u/kosmith)\ **Replies:** 1\ **Last updated:** [May 6, 2024, 7:02am UTC](https://gromacs.bioexcel.eu/t/com-pulling-of-large-groups/9061 "2024-05-06T07:02:36Z")
GROMACS version: 2020.2 GROMACS modification: Yes Hi, I am trying to keep 13 separate 1nm sized dye molecules aggregated by pulling each molecule towards the center of mass of all groups. By indexing all atoms of all 1… --- ## [Steered MD doesn't produce expected force graph](https://gromacs.bioexcel.eu/t/steered-md-doesnt-produce-expected-force-graph/8745)
**Author:** [@gromppuser](https://gromacs.bioexcel.eu/u/gromppuser)\ **Replies:** 1\ **Last updated:** [April 8, 2024, 9:22am UTC](https://gromacs.bioexcel.eu/t/steered-md-doesnt-produce-expected-force-graph/8745 "2024-04-08T09:22:15Z")
GROMACS version: 2022.3 GROMACS modification: No I am running a pulling simulation on my protein/antibody system but the force graph output is not showing a decrease in force after the protein/antibody have separated. … --- ## [Assistance Needed with Pulling a Protein Aggregate Through a Protein Pore](https://gromacs.bioexcel.eu/t/assistance-needed-with-pulling-a-protein-aggregate-through-a-protein-pore/8758)
**Author:** [@com\_gro](https://gromacs.bioexcel.eu/u/com_gro)\ **Replies:** 1\ **Last updated:** [April 1, 2024, 10:22pm UTC](https://gromacs.bioexcel.eu/t/assistance-needed-with-pulling-a-protein-aggregate-through-a-protein-pore/8758 "2024-04-01T22:22:12Z")
Hello everyone, I’m working on a molecular dynamics simulation in GROMACS where my objective is to pull an entire protein aggregate through the central pore of another protein. In my system, represented in a PDB/GRO fil… --- ## [Setting pull\_coord1\_geometry = distance vs pull\_coord1\_geometry = direction](https://gromacs.bioexcel.eu/t/setting-pull-coord1-geometry-distance-vs-pull-coord1-geometry-direction/8709)
**Author:** [@Karis](https://gromacs.bioexcel.eu/u/Karis)\ **Replies:** 0\ **Last updated:** [March 27, 2024, 7:35am UTC](https://gromacs.bioexcel.eu/t/setting-pull-coord1-geometry-distance-vs-pull-coord1-geometry-direction/8709 "2024-03-27T07:35:54Z")
I’m trying to set up a constant-force pulling simulation but was a little confused on the difference between setting the mdp parameter pull\_coord1\_geometry to distance or direction. My understanding is that for distance,… --- ## [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… [Next page](https://gromacs.bioexcel.eu/tag/pull-code/45.md?match_all_tags=true&page=1&tags%5B%5D=pull-code)