# Request for Free Energy Integration Files Using Dummy Atoms

**URL:** <https://gromacs.bioexcel.eu/t/request-for-free-energy-integration-files-using-dummy-atoms/8169>\
**Category:** User discussions\
**Tags:** mdp-parameters, free-energy\
**Created:** [January 29, 2024, 2:51pm UTC](https://gromacs.bioexcel.eu/t/request-for-free-energy-integration-files-using-dummy-atoms/8169 "2024-01-29T14:51:34Z")\
**Posts on this page:** 4\
**Page:** 1

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**Author:** ![yehon](https://avatars.discourse-cdn.com/v4/letter/y/e99b99/32.png) [@yehon](https://gromacs.bioexcel.eu/u/yehon)\
**Post date:** [January 29, 2024, 2:51pm UTC](https://gromacs.bioexcel.eu/t/request-for-free-energy-integration-files-using-dummy-atoms/8169/1 "2024-01-29T14:51:34Z")

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GROMACS version: 2021.2  
GROMACS modification: No  
Hello everyone,  
I’m looking for some assistance with relative free energy integration using dummy atoms. If anyone could share `.itp` and `.mdp` files that they’ve successfully used for this purpose, it would be a great help. Additionally, if you have a `forcefield.itp` that details the interactions of the dummy atoms, that would also be beneficial.

I already did it using the following itp and mdp files (here I put only the production step):  
[NC9toNC5\_itpfile.top](https://gromacs.bioexcel.eu/uploads/short-url/msvcXywEVPIC6wOHdhOMOSn7cCy.top) (20.1 KB)  
[md.mdp](https://gromacs.bioexcel.eu/uploads/short-url/e8gIYIgaRo4mYyUjdTQ3Lv1pk3m.mdp) (3.6 KB)

However, the result is far from the result of substraction of two solvation free energy of those ligands (using ‘couple-intramol = no’).  
To keep it brief, it would be really useful if someone could provide an example of an `.itp` file that works correctly using dummy atoms. I’ve found some `.mdp` files online but not an appropriate `.itp` file.

Thanks in advance,  
My mail is: yehon.levy@mail.huji.ac.il

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**Author:** ![milosz.wieczor](https://avatars.discourse-cdn.com/v4/letter/m/b19c9b/32.png) [@milosz.wieczor](https://gromacs.bioexcel.eu/u/milosz.wieczor)\
**Post date:** [January 29, 2024, 9:00pm UTC](https://gromacs.bioexcel.eu/t/request-for-free-energy-integration-files-using-dummy-atoms/8169/2 "2024-01-29T21:00:36Z")

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Hi, [the pmx webserver](http://pmx.mpibpc.mpg.de/) is a great tool for creating alchemical topologies for free energy calculations. For most mutations it creates a full “dual topology”, but if I remember correctly, purine-purine or pyrimidine-pyrimidine mutations [in DNA](http://pmx.mpibpc.mpg.de/dna_webserver.html) follow the “single topology” approach too. You can then use the outputs to get familiar with the format.

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**Author:** ![yehon](https://avatars.discourse-cdn.com/v4/letter/y/e99b99/32.png) [@yehon](https://gromacs.bioexcel.eu/u/yehon)\
**Post date:** [February 3, 2024, 4:20pm UTC](https://gromacs.bioexcel.eu/t/request-for-free-energy-integration-files-using-dummy-atoms/8169/3 "2024-02-03T16:20:11Z")

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Thank you for the insight. I looked at the files on the PMX website. My problem actually was that I removed the Coulomb and van der Waals interactions together, not separately.

I would like to ask another question. I started to write the script for the merged topology by myself; however, I prefer to use something built-in. Can I get advise please on the most commonly used and simplest methods to do this in GROMACS? (I’m using CGenFF and simulating graft carbon chain ligands.)

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**Author:** ![milosz.wieczor](https://avatars.discourse-cdn.com/v4/letter/m/b19c9b/32.png) [@milosz.wieczor](https://gromacs.bioexcel.eu/u/milosz.wieczor)\
**Post date:** [February 3, 2024, 8:08pm UTC](https://gromacs.bioexcel.eu/t/request-for-free-energy-integration-files-using-dummy-atoms/8169/4 "2024-02-03T20:08:10Z")

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It really depends, I remember e.g. there was [this tool](https://github.com/drazen-petrov/SMArt) for finding common substructures and making them into alchemical topologies, and perhaps a few more, but I never tested them myself.

For simple but routine modifications, or perhaps to build a custom workflow while avoiding re-implementing all the topology-related nuisances, I added a few simple routines [in my own library](https://gitlab.com/KomBioMol/gromologist#adding-alchemical-b-states), nothing too general though. If needed, I can always consider adding some simple functions.