# \#pmx **URL:** https://ask.bioexcel.eu/tag/pmx/3.md [Latest](https://ask.bioexcel.eu/latest.md) · [Categories](https://ask.bioexcel.eu/categories.md) · [Tags](https://ask.bioexcel.eu/tags.md) --- ## [NVT vs NPT for Non-Equilibrium Switching in pmx/GROMACS](https://ask.bioexcel.eu/t/nvt-vs-npt-for-non-equilibrium-switching-in-pmx-gromacs/5980)
**Author:** [@EidRashed](https://ask.bioexcel.eu/u/EidRashed)\ **Replies:** 1\ **Last updated:** [January 26, 2026, 11:19am UTC](https://ask.bioexcel.eu/t/nvt-vs-npt-for-non-equilibrium-switching-in-pmx-gromacs/5980 "2026-01-26T11:19:35Z")
I’m using pmx + GROMACS to run non-equilibrium alchemical free energy calculations for large protein–protein interactions (e.g., ~150 k atoms, like Fc–FcRn). My workflow is essentially: Equilibrate both end states (st… --- ## [Using PMX for ΔΔG on a glycosylated Fc (P238D back-mutation; PDB 3WJJ): viable workflows?](https://ask.bioexcel.eu/t/using-pmx-for-g-on-a-glycosylated-fc-p238d-back-mutation-pdb-3wjj-viable-workflows/5933)
**Author:** [@EidRashed](https://ask.bioexcel.eu/u/EidRashed)\ **Replies:** 5\ **Last updated:** [November 20, 2025, 3:29pm UTC](https://ask.bioexcel.eu/t/using-pmx-for-g-on-a-glycosylated-fc-p238d-back-mutation-pdb-3wjj-viable-workflows/5933 "2025-11-20T15:29:18Z")
Hi all, I’d like to use PMX to compute ΔΔG of binding for an Fc that is N-glycosylated (structure based on PDB: 3WJJ) by reversing the mutation P238D. I know PMX supports Amber and CHARMM family protein force fields out… --- ## [Absolute binding Free energy with NE-MD: Single-step complex leg & Boresch restraint tips](https://ask.bioexcel.eu/t/absolute-binding-free-energy-with-ne-md-single-step-complex-leg-boresch-restraint-tips/5840)
**Author:** [@ehsan](https://ask.bioexcel.eu/u/ehsan)\ **Replies:** 1\ **Last updated:** [August 4, 2025, 8:58am UTC](https://ask.bioexcel.eu/t/absolute-binding-free-energy-with-ne-md-single-step-complex-leg-boresch-restraint-tips/5840 "2025-08-04T08:58:51Z")
Hello PMX developers and users, I’m setting up an absolute binding free energy (ABFE) calculation using non-equilibrium MD with PMX/GROMACS, following the thermodynamic cycle (see attached image). Complex Leg (D → F) … --- ## [PMX alchemical free energy calculation for protein mutation](https://ask.bioexcel.eu/t/pmx-alchemical-free-energy-calculation-for-protein-mutation/5537)
**Author:** [@rakibpharma](https://ask.bioexcel.eu/u/rakibpharma)\ **Replies:** 1\ **Last updated:** [March 25, 2025, 12:34pm UTC](https://ask.bioexcel.eu/t/pmx-alchemical-free-energy-calculation-for-protein-mutation/5537 "2025-03-25T12:34:49Z")
I am trying to reproduce the results ΔΔG of protein mutation (W6F), that you have provided in Protein mutation — pmx documentation. I have used devlop branch of pmx for alchemical calculation. I am using the parameters … --- ## [Pmx ligandHybrid error](https://ask.bioexcel.eu/t/pmx-ligandhybrid-error/5441)
**Author:** [@mukherjee175](https://ask.bioexcel.eu/u/mukherjee175)\ **Replies:** 7\ **Last updated:** [March 15, 2025, 3:26pm UTC](https://ask.bioexcel.eu/t/pmx-ligandhybrid-error/5441 "2025-03-15T15:26:33Z")
Hi, I was hoping to perform RBFE calculations where I change Phenylalanine (PHE) to an unnatural amino acid 2-methylPhenylalanine(MPH2) using CharmmFF. The mutations supported by pmx are all natural amino acids. I searc… --- ## [PMX Ligand Preparation from Scratch - Atom Types and Parameter Discrepancies](https://ask.bioexcel.eu/t/pmx-ligand-preparation-from-scratch-atom-types-and-parameter-discrepancies/5429)
**Author:** [@jinurajkr](https://ask.bioexcel.eu/u/jinurajkr)\ **Replies:** 2\ **Last updated:** [February 28, 2025, 11:49am UTC](https://ask.bioexcel.eu/t/pmx-ligand-preparation-from-scratch-atom-types-and-parameter-discrepancies/5429 "2025-02-28T11:49:21Z")
Dear All We are writing to you regarding the preparation of ligands from scratch for running in PMX. We obtained the SDF file for the ligand from the following reference: \[https://pubs.acs.org/doi/10.1021/ja512751q\] Ou… --- ## [Example for software feedback](https://ask.bioexcel.eu/t/example-for-software-feedback/5176)
**Author:** [@alevil](https://ask.bioexcel.eu/u/alevil)\ **Replies:** 0\ **Last updated:** [July 5, 2024, 1:18pm UTC](https://ask.bioexcel.eu/t/example-for-software-feedback/5176 "2024-07-05T13:18:25Z")
Topic: Feedback on GROMACS, HADDOCK, BioBB and PMX Feedback: write the features you would like to be implemented in the future and ideas to improve the core applications. Login to post, select the sub-category softwar…