# How to create topology file for amorphous silica?

**URL:** <https://gromacs.bioexcel.eu/t/how-to-create-topology-file-for-amorphous-silica/12388>\
**Category:** User discussions\
**Tags:** forcefield\
**Created:** [July 16, 2025, 1:06pm UTC](https://gromacs.bioexcel.eu/t/how-to-create-topology-file-for-amorphous-silica/12388 "2025-07-16T13:06:50Z")\
**Posts on this page:** 4\
**Page:** 1

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**Author:** ![lilian](https://avatars.discourse-cdn.com/v4/letter/l/b5a626/32.png) [@lilian](https://gromacs.bioexcel.eu/u/lilian)\
**Post date:** [July 16, 2025, 1:06pm UTC](https://gromacs.bioexcel.eu/t/how-to-create-topology-file-for-amorphous-silica/12388/1 "2025-07-16T13:06:50Z")

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GROMACS version: 2019  
GROMACS modification: No

Dear gromacs users,

I have a pdb file containing drug molecules and amorphous silica. I want to do md simulation of this system using gromacs. How to create topology file for silica?

Best

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**Author:** ![lilian](https://avatars.discourse-cdn.com/v4/letter/l/b5a626/32.png) [@lilian](https://gromacs.bioexcel.eu/u/lilian)\
**Post date:** [July 17, 2025, 9:44am UTC](https://gromacs.bioexcel.eu/t/how-to-create-topology-file-for-amorphous-silica/12388/2 "2025-07-17T09:44:34Z")

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My system is as follows:

 ![image](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/2X/c/c4ac262924eaf1a1c3606a74a925f40bae8645a8.png)

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**Author:** ![MichelePellegrino](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/michelepellegrino/32/628_2.png) [@MichelePellegrino](https://gromacs.bioexcel.eu/u/MichelePellegrino)\
**Post date:** [July 18, 2025, 11:47am UTC](https://gromacs.bioexcel.eu/t/how-to-create-topology-file-for-amorphous-silica/12388/3 "2025-07-18T11:47:58Z")

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Hi, which force field are you going to use to simulate the silica substrate? Depending on the answer, the creation of a topology file may be either difficult or impossible.

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**Author:** ![lilian](https://avatars.discourse-cdn.com/v4/letter/l/b5a626/32.png) [@lilian](https://gromacs.bioexcel.eu/u/lilian)\
**Post date:** [July 18, 2025, 1:25pm UTC](https://gromacs.bioexcel.eu/t/how-to-create-topology-file-for-amorphous-silica/12388/4 "2025-07-18T13:25:41Z")

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Hi. Thanks for your answer.

What is your suggestion? Interface? CLAYFF? CVFF?

Which one is the best for my system. Please consider drug molecule being in my system.