# How do you determine the Pull Direction for a GROMACS umbrella sampling simulation to generate the m

**URL:** <https://gromacs.bioexcel.eu/t/how-do-you-determine-the-pull-direction-for-a-gromacs-umbrella-sampling-simulation-to-generate-the-m/7741>\
**Category:** User discussions\
**Tags:** umbrella-sampling\
**Created:** [November 27, 2023, 6:52pm UTC](https://gromacs.bioexcel.eu/t/how-do-you-determine-the-pull-direction-for-a-gromacs-umbrella-sampling-simulation-to-generate-the-m/7741 "2023-11-27T18:52:41Z")\
**Posts on this page:** 3\
**Page:** 1

<div class="post-metadata">

**Author:** ![unit\_vector](https://avatars.discourse-cdn.com/v4/letter/u/9de0a6/32.png) [@unit\_vector](https://gromacs.bioexcel.eu/u/unit_vector)\
**Post date:** [November 27, 2023, 6:52pm UTC](https://gromacs.bioexcel.eu/t/how-do-you-determine-the-pull-direction-for-a-gromacs-umbrella-sampling-simulation-to-generate-the-m/7741/1 "2023-11-27T18:52:41Z")

</div>

GROMACS version: 2023.2  
GROMACS modification: No

I am trying to calculate the free energy between a protein and aptamer using GROMACS. Literature has indicated that one of the best way to do so is by performing an umbrella sampling MD simulation that involves a non-equilibrium pulling simulation that pulls the protein and aptamer apart. I have been running these simulations on certain protein-aptamer complexes but some of the free energy values that I am getting do not match the experimental free energy values from biology experiments. I am thinking that perhaps the pulling direction that I chose was not the best pulling direction. How do I determine the best/correct pulling direction?

Furthermore, what are the common sources of error when performing these umbrella sampling simulations? How do I make my simulations more accurate?

I am essentially using the procedure in this tutorial [Umbrella Sampling](http://www.mdtutorials.com/gmx/umbrella/index.html) by Justin A. Lemkul, Ph.D., Virginia Tech Department of Biochemistry, except I am performing it on a protein-aptamer complex.

---

<div class="post-metadata">

**Author:** ![FarzaneJP](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/farzanejp/32/1211_2.png) [@FarzaneJP](https://gromacs.bioexcel.eu/u/FarzaneJP)\
**Post date:** [November 28, 2023, 7:53am UTC](https://gromacs.bioexcel.eu/t/how-do-you-determine-the-pull-direction-for-a-gromacs-umbrella-sampling-simulation-to-generate-the-m/7741/2 "2023-11-28T07:53:20Z")

</div>

Please check out our latest GROMACS tutorials for additional information: [**new GROMACS tutorials**](https://tutorials.gromacs.org/docs/umbrella-sampling.html).  
\*\* You might also want to explore this link: [Potential of mean force using AWH method — GROMACS tutorials https://tutorials.gromacs.org documentation](https://tutorials.gromacs.org/awh-tutorial.html)

---

<div class="post-metadata">

**Author:** ![unit\_vector](https://avatars.discourse-cdn.com/v4/letter/u/9de0a6/32.png) [@unit\_vector](https://gromacs.bioexcel.eu/u/unit_vector)\
**Post date:** [January 5, 2024, 6:09am UTC](https://gromacs.bioexcel.eu/t/how-do-you-determine-the-pull-direction-for-a-gromacs-umbrella-sampling-simulation-to-generate-the-m/7741/3 "2024-01-05T06:09:34Z")

</div>

When I am running these tutorials, how do I know that I have run it correctly and that the results I am getting make sense in the context of the simulation parameters?