# How to run a simulation with input files?

**URL:** <https://gromacs.bioexcel.eu/t/how-to-run-a-simulation-with-input-files/625>\
**Category:** User discussions\
**Created:** [August 5, 2020, 12:21pm UTC](https://gromacs.bioexcel.eu/t/how-to-run-a-simulation-with-input-files/625 "2020-08-05T12:21:09Z")\
**Posts on this page:** 5\
**Page:** 1

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**Author:** ![Amo1997](https://avatars.discourse-cdn.com/v4/letter/a/ad7895/32.png) [@Amo1997](https://gromacs.bioexcel.eu/u/Amo1997)\
**Post date:** [August 5, 2020, 12:21pm UTC](https://gromacs.bioexcel.eu/t/how-to-run-a-simulation-with-input-files/625/1 "2020-08-05T12:21:09Z")

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

Hi,

I have downloaded the necessary files (equilibration.inp and production.inp files) to carry out a simulation on Gromacs from the Multicomponent Assembler in Charmm in the form of the tgz. file and this was extracted. However, in order to run the simulation, I believe the files need to be in an mdp format?

The Job Retriever ID is: 9621133563

I would appreciate any advice on on how to proceed with the simulation on Ubuntu using the files obtained.

Many Thanks,

Amo

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**Author:** ![cblau](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/cblau/32/5_2.png) [@cblau](https://gromacs.bioexcel.eu/u/cblau)\
**Post date:** [August 5, 2020, 3:06pm UTC](https://gromacs.bioexcel.eu/t/how-to-run-a-simulation-with-input-files/625/2 "2020-08-05T15:06:16Z")

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Hi Amo,

It seems like you received a charmm input file, GROMACS uses no .inp files, but instead files like .top and .itp for molecule topologies and .gro, .pdb for structures and .mdp for simulation parameter settings.

Unfortuntately I don’t have much experience with converting CHARMM parameters to GROMACS, other form users or google might help you further here.

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**Author:** ![newbie](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/newbie/32/283_2.png) [@newbie](https://gromacs.bioexcel.eu/u/newbie)\
**Post date:** [August 7, 2020, 12:05am UTC](https://gromacs.bioexcel.eu/t/how-to-run-a-simulation-with-input-files/625/3 "2020-08-07T00:05:16Z")

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Hi. I used CHARMM-GUI before. It had provided all of the input files that I wanted in “gromacs folder”! Maybe it’s better to regenerate your structure seperatly for GROMACS and AMMBER and choose forcefields which are suitable for each programm.

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**Author:** ![Amo1997](https://avatars.discourse-cdn.com/v4/letter/a/ad7895/32.png) [@Amo1997](https://gromacs.bioexcel.eu/u/Amo1997)\
**Post date:** [August 7, 2020, 11:09am UTC](https://gromacs.bioexcel.eu/t/how-to-run-a-simulation-with-input-files/625/4 "2020-08-07T11:09:27Z")

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Hi,

Thank you for your reply. I would like to carry out a simulation of Insulin against a silica surface, but would that not require them to be together?

Also, in CHARMM-GUI, I selected to receive my files as in Gromacs format but I get an error - ‘ISC4’.

If I follow your proposed method to regenerate my structure then what input generator would I utilise on CHARMM-GUI?

I would appreciate any advice as I am newbie to this program and currently stuck and cannot report back to my colleague for advice as they are out of office.

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**Author:** ![newbie](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/newbie/32/283_2.png) [@newbie](https://gromacs.bioexcel.eu/u/newbie)\
**Post date:** [August 7, 2020, 12:43pm UTC](https://gromacs.bioexcel.eu/t/how-to-run-a-simulation-with-input-files/625/5 "2020-08-07T12:43:50Z")

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> [@Amo1997](#):
>
> Also, in CHARMM-GUI, I selected to receive my files as in Gromacs format but I get an error - ‘ISC4’.

Maybe it’s better to direct this problem to charmm-gui providers.

> [@Amo1997](#):
>
> If I follow your proposed method to regenerate my structure then what input generator would I utilise on CHARMM-GUI?

I’m not experienced enough in simulation as well, I used charmm-gui to generate complex micelle-protein, but as it mentioned in charmm-gui for modeling Silica: bulk minerals (α-quartz, α-cristobalite) as well as surfaces of different degree of ionization for specific pH values and particle sizes, you can use Nanomaterial Modeler.