# Pathogen membrane and peptides simulation

**URL:** <https://gromacs.bioexcel.eu/t/pathogen-membrane-and-peptides-simulation/10907>\
**Category:** User discussions\
**Tags:** simulation-setup\
**Created:** [December 27, 2024, 2:53pm UTC](https://gromacs.bioexcel.eu/t/pathogen-membrane-and-peptides-simulation/10907 "2024-12-27T14:53:15Z")\
**Posts on this page:** 5\
**Page:** 1

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**Author:** ![xander](https://avatars.discourse-cdn.com/v4/letter/x/f05b48/32.png) [@xander](https://gromacs.bioexcel.eu/u/xander)\
**Post date:** [December 27, 2024, 2:53pm UTC](https://gromacs.bioexcel.eu/t/pathogen-membrane-and-peptides-simulation/10907/1 "2024-12-27T14:53:15Z")

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i have a fungal membrane and an antimicrobial peptide, it possible for me to perform simulations? if yes, please provide the hints and guidance

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**Author:** ![MiSSSD](https://avatars.discourse-cdn.com/v4/letter/m/eb8c5e/32.png) [@MiSSSD](https://gromacs.bioexcel.eu/u/MiSSSD)\
**Post date:** [March 4, 2026, 3:19am UTC](https://gromacs.bioexcel.eu/t/pathogen-membrane-and-peptides-simulation/10907/2 "2026-03-04T03:19:49Z")

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Hi

Were you able to perform simulations?  
If yes … can you guide me as to how to do it?

Thanks a lot !

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**Author:** ![scinikhil](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/scinikhil/32/3483_2.png) [@scinikhil](https://gromacs.bioexcel.eu/u/scinikhil)\
**Post date:** [March 29, 2026, 5:55am UTC](https://gromacs.bioexcel.eu/t/pathogen-membrane-and-peptides-simulation/10907/3 "2026-03-29T05:55:30Z")

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It is possible where do you stand now? what is the issue?

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**Author:** ![xander](https://avatars.discourse-cdn.com/v4/letter/x/f05b48/32.png) [@xander](https://gromacs.bioexcel.eu/u/xander)\
**Post date:** [March 29, 2026, 8:04am UTC](https://gromacs.bioexcel.eu/t/pathogen-membrane-and-peptides-simulation/10907/4 "2026-03-29T08:04:51Z")

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Yes, i did the simulation, i used CHARM-GUI to mimic the membrane, and then i placed this peptide close to the membrane, i used pymol for this, therafter, i uploaded the complex to the CHARM-GUI online server to gerenarate input parameters snd files for simulation in GROMACS.

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<div class="post-metadata">

**Author:** ![xander](https://avatars.discourse-cdn.com/v4/letter/x/f05b48/32.png) [@xander](https://gromacs.bioexcel.eu/u/xander)\
**Post date:** [March 29, 2026, 8:06am UTC](https://gromacs.bioexcel.eu/t/pathogen-membrane-and-peptides-simulation/10907/5 "2026-03-29T08:06:25Z")

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Yes, i did the simulation, i used CHARM-GUI to mimic the membrane, and then i placed this peptide close to the membrane, i used pymol for this, therafter, i uploaded the complex to the CHARM-GUI online server to gerenarate input parameters snd files for simulation in GROMACS.