# MD Simulation of protein with ionic liquid

**URL:** https://gromacs.bioexcel.eu/t/md-simulation-of-protein-with-ionic-liquid/9674
**Category:** User discussions
**Created:** [July 18, 2024, 5:03am UTC](https://gromacs.bioexcel.eu/t/md-simulation-of-protein-with-ionic-liquid/9674 "2024-07-18T05:03:03Z")
**Posts on this page:** 4
**Page:** 1

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### Author: ![ABHI7](https://avatars.discourse-cdn.com/v4/letter/a/bc8723/32.png) [@ABHI7](https://gromacs.bioexcel.eu/u/ABHI7)
#### Post date: [July 18, 2024, 5:03am UTC](https://gromacs.bioexcel.eu/t/md-simulation-of-protein-with-ionic-liquid/9674/1 "2024-07-18T05:03:03Z")

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GROMACS version:  
GROMACS modification: Yes/No  
Here post your question

Im performing MD simulation of Insulin protein with Choline-Geranate ionic liquid by preparing different system of different mole fraction.  
the system was prepared using “gmx insert-molecules” and the number of solvent was restricted by using “-maxsol”.  
I perform NVT followed by NPT equilibrium for 10ns.

For testing Im performing simulation at 15ns.

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### Author: ![ABHI7](https://avatars.discourse-cdn.com/v4/letter/a/bc8723/32.png) [@ABHI7](https://gromacs.bioexcel.eu/u/ABHI7)
#### Post date: [July 18, 2024, 5:04am UTC](https://gromacs.bioexcel.eu/t/md-simulation-of-protein-with-ionic-liquid/9674/2 "2024-07-18T05:04:37Z")

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![WhatsApp Image 2024-07-11 at 19.53.17](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/2X/c/c33cdb5c2dc31a72d19a4cc9fb6c5fbc3d4d5e90.jpeg)  
This is the snapshot of NPT equilibrium.

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### Author: ![ABHI7](https://avatars.discourse-cdn.com/v4/letter/a/bc8723/32.png) [@ABHI7](https://gromacs.bioexcel.eu/u/ABHI7)
#### Post date: [July 18, 2024, 5:12am UTC](https://gromacs.bioexcel.eu/t/md-simulation-of-protein-with-ionic-liquid/9674/3 "2024-07-18T05:12:36Z")

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![WhatsApp Image 2024-07-11 at 19.53.17(1)](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/2X/5/51b7645b97eccba80ea67ad011540988ab936ca7.jpeg)  
this is the snapshot of MD.gro output .  
(the box size was reduced after NPT and MD run)  
My question is that “am I following right procedure or wrong?”  
please suggest me, “if I following wrong procedure then guide me what procedure should I follow?”

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### Author: ![rpsingh](https://avatars.discourse-cdn.com/v4/letter/r/c57346/32.png) [@rpsingh](https://gromacs.bioexcel.eu/u/rpsingh)
#### Post date: [July 23, 2024, 3:08pm UTC](https://gromacs.bioexcel.eu/t/md-simulation-of-protein-with-ionic-liquid/9674/4 "2024-07-23T15:08:02Z")

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First prepare a solvent only box (using gmx insert-molecules or Packmol), run minimisation and equilibration steps and then a production run. The duration of production run can be anything from 5 ns to longer depending on your solvent characteristics. I have found that water and small organic molecules typically require 2-5 ns.  
Use the equilibrated solvent box with gmx solvate.

Regards,  
Raman