# GROMACS tutorial problem

**URL:** <https://gromacs.bioexcel.eu/t/gromacs-tutorial-problem/6284>\
**Category:** User discussions\
**Created:** [April 26, 2023, 10:41am UTC](https://gromacs.bioexcel.eu/t/gromacs-tutorial-problem/6284 "2023-04-26T10:41:41Z")\
**Posts on this page:** 8\
**Page:** 1

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**Author:** ![EOrfanakis](https://avatars.discourse-cdn.com/v4/letter/e/7cd45c/32.png) [@EOrfanakis](https://gromacs.bioexcel.eu/u/EOrfanakis)\
**Post date:** [April 26, 2023, 10:41am UTC](https://gromacs.bioexcel.eu/t/gromacs-tutorial-problem/6284/1 "2023-04-26T10:41:42Z")

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GROMACS version: 2023  
GROMACS modification: No  
Here post your question  
GROMACS Tutorial  
Building Biphasic Systems  
I have made this tutorial with biphasic system and the referenced files but i cannot do energy minimization as i dont have the topoloy for the whole system. What can i do?

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**Author:** ![Karis](https://avatars.discourse-cdn.com/v4/letter/k/ed8c4c/32.png) [@Karis](https://gromacs.bioexcel.eu/u/Karis)\
**Post date:** [April 28, 2023, 6:33am UTC](https://gromacs.bioexcel.eu/t/gromacs-tutorial-problem/6284/2 "2023-04-28T06:33:30Z")

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Are you referring to the energy minimization of chx\_box.gro? chx.top should work as the topology file, you just need to change the number of molecules at the bottom of the chx.top file under [molecules] to match the number you generated for chx\_box.gro. For example, I used random insertion and got a box of 1039 CHX molecules, so that’s the number I used

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**Author:** ![jalemkul](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/jalemkul/32/18_2.png) [@jalemkul](https://gromacs.bioexcel.eu/u/jalemkul)\
**Post date:** [April 28, 2023, 1:39pm UTC](https://gromacs.bioexcel.eu/t/gromacs-tutorial-problem/6284/3 "2023-04-28T13:39:23Z")

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There is a topology file provided in the tutorial and as Karis notes, you may just have to update the number of CHX molecules in it. Then if you add water as the tutorial shows you via `gmx solvate`, it will update the topology with the number of water molecules it added. The `#include` statement for the SPC topology is already in `chx.top` in preparation for this step.

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**Author:** ![EOrfanakis](https://avatars.discourse-cdn.com/v4/letter/e/7cd45c/32.png) [@EOrfanakis](https://gromacs.bioexcel.eu/u/EOrfanakis)\
**Post date:** [April 30, 2023, 10:39am UTC](https://gromacs.bioexcel.eu/t/gromacs-tutorial-problem/6284/4 "2023-04-30T10:39:27Z")

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Thank you for your replies! I will try them and update you!

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**Author:** ![Dedunu](https://avatars.discourse-cdn.com/v4/letter/d/bc79bd/32.png) [@Dedunu](https://gromacs.bioexcel.eu/u/Dedunu)\
**Post date:** [August 18, 2023, 3:51am UTC](https://gromacs.bioexcel.eu/t/gromacs-tutorial-problem/6284/5 "2023-08-18T03:51:04Z")

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Dear Sir, I have a follow up question related to this building a biphasic system GROMACS tutorial. So when doing NVT and NPT equilibration can I use the same chx.top file given in the tutorial. And am I supposed to delete “define = -DPOSRES” line in the nvt.mdp and npt.mdp files since I don’t have a posre.itp file given in the tutorial? please help me with this. Thank you.

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**Author:** ![gottlib](https://avatars.discourse-cdn.com/v4/letter/g/0ea827/32.png) [@gottlib](https://gromacs.bioexcel.eu/u/gottlib)\
**Post date:** [September 21, 2023, 4:47pm UTC](https://gromacs.bioexcel.eu/t/gromacs-tutorial-problem/6284/6 "2023-09-21T16:47:57Z")

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Could you suggest a correct way to get index file for nvt.mdp? The problem is that the generated system appears as 3 different group with just one kind of residue. How is it possible to obtain 2 groups? Thanks!

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**Author:** ![jalemkul](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/jalemkul/32/18_2.png) [@jalemkul](https://gromacs.bioexcel.eu/u/jalemkul)\
**Post date:** [September 21, 2023, 4:59pm UTC](https://gromacs.bioexcel.eu/t/gromacs-tutorial-problem/6284/7 "2023-09-21T16:59:27Z")

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> [@gottlib](#):
>
> How is it possible to obtain 2 groups?

You don’t need two groups if you’re referring to `tc-grps`. Just set `tc-grps = system`.

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**Author:** ![gottlib](https://avatars.discourse-cdn.com/v4/letter/g/0ea827/32.png) [@gottlib](https://gromacs.bioexcel.eu/u/gottlib)\
**Post date:** [September 27, 2023, 3:01pm UTC](https://gromacs.bioexcel.eu/t/gromacs-tutorial-problem/6284/8 "2023-09-27T15:01:54Z")

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Thanks a lot! It worked.