# BioExcel Webinar **URL:** https://ask.bioexcel.eu/c/bioexcel-webinar/56.md [Latest](https://ask.bioexcel.eu/latest.md) · [Categories](https://ask.bioexcel.eu/categories.md) · [Tags](https://ask.bioexcel.eu/tags.md) --- ## [About the BioExcel Webinar category](https://ask.bioexcel.eu/t/about-the-bioexcel-webinar-category/4477)
**Author:** [@alevil](https://ask.bioexcel.eu/u/alevil)\ **Replies:** 0
Here you ask questions to the BioExcel Webinar speakers. After each BioExcel Webinar, you can discuss the webinar topic with speaker for one week. --- ## [Webinar #98: Conformational ensembles of intrinsically disordered regions and proteins (2026-05-26)](https://ask.bioexcel.eu/t/webinar-98-conformational-ensembles-of-intrinsically-disordered-regions-and-proteins-2026-05-26/6131)
**Author:** [@alevil](https://ask.bioexcel.eu/u/alevil)\ **Replies:** 4\ **Last updated:** [May 27, 2026, 12:58pm UTC](https://ask.bioexcel.eu/t/webinar-98-conformational-ensembles-of-intrinsically-disordered-regions-and-proteins-2026-05-26/6131 "2026-05-27T12:58:08Z")
Intrinsically disordered proteins and regions (collectively IDRs) are pervasive across proteomes in all kingdoms of life, help shape biological functions, and are involved in numerous diseases \[1\]. IDRs populate a divers… --- ## [Wabinar #97: Driving forces in biomolecular condensates from atomistic simulations of model peptides](https://ask.bioexcel.eu/t/wabinar-97-driving-forces-in-biomolecular-condensates-from-atomistic-simulations-of-model-peptides/6103)
**Author:** [@alevil](https://ask.bioexcel.eu/u/alevil)\ **Replies:** 1\ **Last updated:** [May 12, 2026, 2:25pm UTC](https://ask.bioexcel.eu/t/wabinar-97-driving-forces-in-biomolecular-condensates-from-atomistic-simulations-of-model-peptides/6103 "2026-05-12T14:25:23Z")
Abstract: Short peptides have been instrumental as models for more complex systems. Studying short peptides, we have gained understanding of fundamental folding events like alpha helix nucleation or hairpin folding, and … --- ## [Webinar #95 DynaPIN: A Tool for Characterizing Dynamic Protein Interfaces (2026-04-28)](https://ask.bioexcel.eu/t/webinar-95-dynapin-a-tool-for-characterizing-dynamic-protein-interfaces-2026-04-28/6081)
**Author:** [@alevil](https://ask.bioexcel.eu/u/alevil)\ **Replies:** 0\ **Last updated:** [April 20, 2026, 3:04pm UTC](https://ask.bioexcel.eu/t/webinar-95-dynapin-a-tool-for-characterizing-dynamic-protein-interfaces-2026-04-28/6081 "2026-04-20T15:04:20Z")
Abstract: Static structural models often fail to capture the dynamic mechanisms of protein interactions. To address this, we introduce DynaPIN, an open-source pipeline for extracting dynamic interface fingerprints from m… --- ## [Webinar #96: Multiscale simulation of biomembranes: shape, structure and cellular function](https://ask.bioexcel.eu/t/webinar-96-multiscale-simulation-of-biomembranes-shape-structure-and-cellular-function/6073)
**Author:** [@alevil](https://ask.bioexcel.eu/u/alevil)\ **Replies:** 2\ **Last updated:** [April 14, 2026, 4:32pm UTC](https://ask.bioexcel.eu/t/webinar-96-multiscale-simulation-of-biomembranes-shape-structure-and-cellular-function/6073 "2026-04-14T16:32:51Z")
Biological membranes exhibit intricate, large-scale dynamical architectures that are intimately coupled to cellular function, and abnormal membrane organization is implicated in many diseases. These structures arise from… --- ## [BioExcel Webinar #91: From Quick Script to Reproducible Workflow: Small Research Software Engineering Habits, Big Impact](https://ask.bioexcel.eu/t/bioexcel-webinar-91-from-quick-script-to-reproducible-workflow-small-research-software-engineering-habits-big-impact/6005)
**Author:** [@alevil](https://ask.bioexcel.eu/u/alevil)\ **Replies:** 0\ **Last updated:** [February 17, 2026, 1:08pm UTC](https://ask.bioexcel.eu/t/bioexcel-webinar-91-from-quick-script-to-reproducible-workflow-small-research-software-engineering-habits-big-impact/6005 "2026-02-17T13:08:24Z")
Reproducible analysis pipelines sound great in theory, but what does that look like in the life of a busy researcher doing biomolecular system analysis with a “quick and dirty” script on their laptop computer? In this we… --- ## [BioExcel Webinar #89 VTX: From Real-Time high performance molecular structure and dynamics visualization to integrative modeling of massive molecular systems](https://ask.bioexcel.eu/t/bioexcel-webinar-89-vtx-from-real-time-high-performance-molecular-structure-and-dynamics-visualization-to-integrative-modeling-of-massive-molecular-systems/5984)
**Author:** [@alevil](https://ask.bioexcel.eu/u/alevil)\ **Replies:** 0\ **Last updated:** [January 26, 2026, 10:35am UTC](https://ask.bioexcel.eu/t/bioexcel-webinar-89-vtx-from-real-time-high-performance-molecular-structure-and-dynamics-visualization-to-integrative-modeling-of-massive-molecular-systems/5984 "2026-01-26T10:35:58Z")
Title VTX: From Real-Time high performance molecular structure and dynamics visualization to integrative modeling of massive molecular systems Molecular visualization is a critical task usually performed by structural b… --- ## [BioExcel Webinar #88: Molywood-GUI: A graphical interface for effortless molecular movie design in VMD (2025-12-16)](https://ask.bioexcel.eu/t/bioexcel-webinar-88-molywood-gui-a-graphical-interface-for-effortless-molecular-movie-design-in-vmd-2025-12-16/5963)
**Author:** [@alevil](https://ask.bioexcel.eu/u/alevil)\ **Replies:** 1\ **Last updated:** [December 16, 2025, 3:10pm UTC](https://ask.bioexcel.eu/t/bioexcel-webinar-88-molywood-gui-a-graphical-interface-for-effortless-molecular-movie-design-in-vmd-2025-12-16/5963 "2025-12-16T15:10:39Z")
Abstract For a long time, designing and rendering molecular movies required expert knowledge, from advanced scripting and editing skills to detailed knowledge of the inner workings of renderers and visualizing software. … --- ## [BioExcel Webinar #84: Perspective on simulating whole cells with Martini](https://ask.bioexcel.eu/t/bioexcel-webinar-84-perspective-on-simulating-whole-cells-with-martini/5485)
**Author:** [@alevil](https://ask.bioexcel.eu/u/alevil)\ **Replies:** 1\ **Last updated:** [May 28, 2025, 9:41am UTC](https://ask.bioexcel.eu/t/bioexcel-webinar-84-perspective-on-simulating-whole-cells-with-martini/5485 "2025-05-28T09:41:09Z")
As trained physical chemist (PhD in 1994), Siewert-Jan Marrink specialized in the use of computational modelling. Central aims of his research are: i) to unravel the lateral organization principles of biological membrane… --- ## [BioExcel Webinar #86 : MiMiC: A high-performance framework for multiscale molecular dynamics simulations](https://ask.bioexcel.eu/t/bioexcel-webinar-86-mimic-a-high-performance-framework-for-multiscale-molecular-dynamics-simulations/5662)
**Author:** [@alevil](https://ask.bioexcel.eu/u/alevil)\ **Replies:** 2\ **Last updated:** [May 26, 2025, 1:26pm UTC](https://ask.bioexcel.eu/t/bioexcel-webinar-86-mimic-a-high-performance-framework-for-multiscale-molecular-dynamics-simulations/5662 "2025-05-26T13:26:01Z")
These days, computational chemists can choose from a wide variety of software packages, each with its own unique features and strengths. Many of these programs also offer some support for modeling chemical processes requ… --- ## [(@marco.giulini) BioexcelWebinar#85: Modeling antibodies in the post-Alphafold era: Where are we now?](https://ask.bioexcel.eu/t/marco-giulini-bioexcelwebinar-85-modeling-antibodies-in-the-post-alphafold-era-where-are-we-now/5582)
**Author:** [@Alexandro926178](https://ask.bioexcel.eu/u/Alexandro926178)\ **Replies:** 17\ **Last updated:** [May 13, 2025, 4:51pm UTC](https://ask.bioexcel.eu/t/marco-giulini-bioexcelwebinar-85-modeling-antibodies-in-the-post-alphafold-era-where-are-we-now/5582 "2025-05-13T16:51:30Z")
Dear Marco Giulini, First of all, congratulations on your excellent participation! I am working with computational methods to elucidate the allergic mechanism triggered by polyethylene glycol used in the formulation of t… --- ## [BioExcel Webinar #83 Restoring Protein Glycosylation with GlycoShape](https://ask.bioexcel.eu/t/bioexcel-webinar-83-restoring-protein-glycosylation-with-glycoshape/5468)
**Author:** [@alevil](https://ask.bioexcel.eu/u/alevil)\ **Replies:** 0\ **Last updated:** [March 11, 2025, 1:47pm UTC](https://ask.bioexcel.eu/t/bioexcel-webinar-83-restoring-protein-glycosylation-with-glycoshape/5468 "2025-03-11T13:47:03Z")
The introduction of machine learning (ML) for protein structure prediction1,2 revolutionized structural biology, boosting our ability to source and resolve protein structures, and broadening the potential for therapeutic… --- ## [BioExcel Webinar #80: Accounting for protein and ligand flexibility in molecular docking and virtual screening of challenging targets](https://ask.bioexcel.eu/t/bioexcel-webinar-80-accounting-for-protein-and-ligand-flexibility-in-molecular-docking-and-virtual-screening-of-challenging-targets/5407)
**Author:** [@alevil](https://ask.bioexcel.eu/u/alevil)\ **Replies:** 1\ **Last updated:** [January 31, 2025, 10:57am UTC](https://ask.bioexcel.eu/t/bioexcel-webinar-80-accounting-for-protein-and-ligand-flexibility-in-molecular-docking-and-virtual-screening-of-challenging-targets/5407 "2025-01-31T10:57:09Z")
BioExcel Webinar #80: Accounting for protein and ligand flexibility in molecular docking and virtual screening of challenging targets by Attilio Vargiu @vargiu Knowledge of atomic-level structures of ligand-protein co… --- ## [About trajectory size](https://ask.bioexcel.eu/t/about-trajectory-size/4798)
**Author:** [@alevil](https://ask.bioexcel.eu/u/alevil)\ **Replies:** 2\ **Last updated:** [February 6, 2024, 7:51pm UTC](https://ask.bioexcel.eu/t/about-trajectory-size/4798 "2024-02-06T19:51:15Z")
Hi What will be the file size of the trajectory file ? I mean is big trajectory file is supported ? --- ## [About loading options](https://ask.bioexcel.eu/t/about-loading-options/4799)
**Author:** [@alevil](https://ask.bioexcel.eu/u/alevil)\ **Replies:** 2\ **Last updated:** [February 6, 2024, 7:49pm UTC](https://ask.bioexcel.eu/t/about-loading-options/4799 "2024-02-06T19:49:07Z")
Hi , I have two questions: Is there a possibility to add a stride to the import of .xtc files, like only load every nth frame? And as you said the splicing was inspired by python, does that mean resname(‘ALA’)\[2:8\] selec… --- ## [System requirements](https://ask.bioexcel.eu/t/system-requirements/4796)
**Author:** [@alevil](https://ask.bioexcel.eu/u/alevil)\ **Replies:** 1\ **Last updated:** [February 6, 2024, 4:00pm UTC](https://ask.bioexcel.eu/t/system-requirements/4796 "2024-02-06T16:00:19Z")
Hi, What is the system requirements to run this? Especially the GPU. If a system can generate gromacs trajectories, would it surely also run viamd? --- ## [Saving plots images](https://ask.bioexcel.eu/t/saving-plots-images/4795)
**Author:** [@alevil](https://ask.bioexcel.eu/u/alevil)\ **Replies:** 1\ **Last updated:** [February 6, 2024, 3:56pm UTC](https://ask.bioexcel.eu/t/saving-plots-images/4795 "2024-02-06T15:56:47Z")
Hi Are there means available in the works for; taking images, making GIFS, recording videos and saving plots? --- ## [About performance](https://ask.bioexcel.eu/t/about-performance/4800)
**Author:** [@alevil](https://ask.bioexcel.eu/u/alevil)\ **Replies:** 1\ **Last updated:** [February 6, 2024, 3:51pm UTC](https://ask.bioexcel.eu/t/about-performance/4800 "2024-02-06T15:51:40Z")
Hi, How good is the performance of the software for loading and reading large trajectories/systems? --- ## [About molecular dynamics simulations](https://ask.bioexcel.eu/t/about-molecular-dynamics-simulations/4801)
**Author:** [@alevil](https://ask.bioexcel.eu/u/alevil)\ **Replies:** 1\ **Last updated:** [February 6, 2024, 3:48pm UTC](https://ask.bioexcel.eu/t/about-molecular-dynamics-simulations/4801 "2024-02-06T15:48:15Z")
Hi, Can we run Molecular dynamics simulations? --- ## [Two questions on VIAMD](https://ask.bioexcel.eu/t/two-questions-on-viamd/4797)
**Author:** [@alevil](https://ask.bioexcel.eu/u/alevil)\ **Replies:** 1\ **Last updated:** [February 6, 2024, 3:44pm UTC](https://ask.bioexcel.eu/t/two-questions-on-viamd/4797 "2024-02-06T15:44:27Z")
Hi, Does VIAMD support .xyz format? For the QM/MM simulations is it possible to analyze molecular orbitals using VIAMD for example using .cube files? --- ## [Question about effective energy in stochastic thermostats](https://ask.bioexcel.eu/t/question-about-effective-energy-in-stochastic-thermostats/4687)
**Author:** [@jfaraudo](https://ask.bioexcel.eu/u/jfaraudo)\ **Replies:** 1\ **Last updated:** [February 6, 2024, 9:25am UTC](https://ask.bioexcel.eu/t/question-about-effective-energy-in-stochastic-thermostats/4687 "2024-02-06T09:25:24Z")
My questions are related to the point you mention about the existence of a conserved quantity for your thermostat and Langevin thermostat. My first question is why you call it effective energy? Is not an energy in a well… --- ## [On Maxwell-Boltzmann distribution](https://ask.bioexcel.eu/t/on-maxwell-boltzmann-distribution/4676)
**Author:** [@alevil](https://ask.bioexcel.eu/u/alevil)\ **Replies:** 0\ **Last updated:** [November 14, 2023, 3:08pm UTC](https://ask.bioexcel.eu/t/on-maxwell-boltzmann-distribution/4676 "2023-11-14T15:08:44Z")
Hi Could the barostat cell rescaling steer the system from the Maxwell-Boltzmann distribution, perhaps by creating locale which radically vioalte the Boltzmann distribution at set temperature? --- ## [Low pressure (e.g 100 Pa)](https://ask.bioexcel.eu/t/low-pressure-e-g-100-pa/4675)
**Author:** [@alevil](https://ask.bioexcel.eu/u/alevil)\ **Replies:** 0\ **Last updated:** [November 14, 2023, 2:39pm UTC](https://ask.bioexcel.eu/t/low-pressure-e-g-100-pa/4675 "2023-11-14T14:39:26Z")
Hi, What thermostat and barostat settings should I use for low pressure (e.g., 100 Pa) simulations NPT? --- ## [Implicit vs explicit solvent](https://ask.bioexcel.eu/t/implicit-vs-explicit-solvent/4674)
**Author:** [@alevil](https://ask.bioexcel.eu/u/alevil)\ **Replies:** 0\ **Last updated:** [November 14, 2023, 2:38pm UTC](https://ask.bioexcel.eu/t/implicit-vs-explicit-solvent/4674 "2023-11-14T14:38:37Z")
Hi what do you suggest use with implicit solvent? --- ## [Liquid and gaseous system](https://ask.bioexcel.eu/t/liquid-and-gaseous-system/4673)
**Author:** [@alevil](https://ask.bioexcel.eu/u/alevil)\ **Replies:** 0\ **Last updated:** [November 14, 2023, 2:35pm UTC](https://ask.bioexcel.eu/t/liquid-and-gaseous-system/4673 "2023-11-14T14:35:40Z")
Could a stochastic thermostat, relative to a strictly deterministic once, generate more entropy in a liquid or gaseous system, biasing the system toward more fluctuation? I mean not in absolute terms only but proportiona… --- ## [About Github link](https://ask.bioexcel.eu/t/about-github-link/4672)
**Author:** [@alevil](https://ask.bioexcel.eu/u/alevil)\ **Replies:** 0\ **Last updated:** [November 14, 2023, 2:34pm UTC](https://ask.bioexcel.eu/t/about-github-link/4672 "2023-11-14T14:34:32Z")
Hi, Can I have the Github link? --- ## [Running RBFE on several molecules](https://ask.bioexcel.eu/t/running-rbfe-on-several-molecules/4484)
**Author:** [@alevil](https://ask.bioexcel.eu/u/alevil)\ **Replies:** 1\ **Last updated:** [September 6, 2023, 8:37am UTC](https://ask.bioexcel.eu/t/running-rbfe-on-several-molecules/4484 "2023-09-06T08:37:01Z")
Hi, How do you get running RBFE on several molecules if the ir not a congeneric series? How do check if the run was ok. --- ## [About SMILES database](https://ask.bioexcel.eu/t/about-smiles-database/4485)
**Author:** [@alevil](https://ask.bioexcel.eu/u/alevil)\ **Replies:** 1\ **Last updated:** [September 6, 2023, 8:34am UTC](https://ask.bioexcel.eu/t/about-smiles-database/4485 "2023-09-06T08:34:38Z")
Hi, How can you make sure that the SMILES database used is complete? How can you account for a specific family of drugs of which there is only a small number of them in the way larger dataset? Thank you :slight\_smile: --- ## [Is maize avalaible for everyone?](https://ask.bioexcel.eu/t/is-maize-avalaible-for-everyone/4486)
**Author:** [@alevil](https://ask.bioexcel.eu/u/alevil)\ **Replies:** 1\ **Last updated:** [September 6, 2023, 8:26am UTC](https://ask.bioexcel.eu/t/is-maize-avalaible-for-everyone/4486 "2023-09-06T08:26:25Z")
Hi, Is maize avalaible for everyone? --- ## [Hardware requirement](https://ask.bioexcel.eu/t/hardware-requirement/4487)
**Author:** [@alevil](https://ask.bioexcel.eu/u/alevil)\ **Replies:** 1\ **Last updated:** [September 6, 2023, 8:18am UTC](https://ask.bioexcel.eu/t/hardware-requirement/4487 "2023-09-06T08:18:36Z")
What is the least hardware requirement to run the program in normal computer ? Or do I need super computer to run? [Next page](https://ask.bioexcel.eu/c/bioexcel-webinar/56.md?page=1)