# AWH Sampling across periodic boundaries

**URL:** <https://gromacs.bioexcel.eu/t/awh-sampling-across-periodic-boundaries/4876>\
**Category:** User discussions\
**Tags:** mdp-parameters, awh\
**Created:** [September 26, 2022, 6:37pm UTC](https://gromacs.bioexcel.eu/t/awh-sampling-across-periodic-boundaries/4876 "2022-09-26T18:37:40Z")\
**Posts on this page:** 4\
**Page:** 1

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**Author:** ![himberts](https://avatars.discourse-cdn.com/v4/letter/h/6a8cbe/32.png) [@himberts](https://gromacs.bioexcel.eu/u/himberts)\
**Post date:** [September 26, 2022, 6:37pm UTC](https://gromacs.bioexcel.eu/t/awh-sampling-across-periodic-boundaries/4876/1 "2022-09-26T18:37:41Z")

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GROMACS version:2022-03  
GROMACS modification: No

I am trying to determine the Potential of mean force profile for a ligand passing through a membrane. I was planning to use gromac’s AWH tool. I would like to pull the ligand through the entire membrane (more than half the box). However, I keep getting error messages indicating that this is not permitted.  
What mdp parameters do I have to use, if I want to pull the molecule through the membrane and across periodic boundaries?

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**Author:** ![hess](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/hess/32/416_2.png) [@hess](https://gromacs.bioexcel.eu/u/hess)\
**Post date:** [September 27, 2022, 7:48am UTC](https://gromacs.bioexcel.eu/t/awh-sampling-across-periodic-boundaries/4876/2 "2022-09-27T07:48:32Z")

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The periodic boundary itself is irrelevant for all method in GROMACS.

What can be problematic is distances that larger than half the box size. I would think you can much a molecule up to half the box size above and below the membrane. Do you get an error when you attempt that?

With AWH you can have a periodic domain when the box size along the dimension you are pulling is fixed. But I think you do not want a periodic domain in your case.

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<div class="post-metadata">

**Author:** ![himberts](https://avatars.discourse-cdn.com/v4/letter/h/6a8cbe/32.png) [@himberts](https://gromacs.bioexcel.eu/u/himberts)\
**Post date:** [September 27, 2022, 11:17am UTC](https://gromacs.bioexcel.eu/t/awh-sampling-across-periodic-boundaries/4876/3 "2022-09-27T11:17:21Z")

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Hi Hess, thanks for the prompt respons. This is very helpful. I pull the molecule along z and we used anisotropic coupling in umbrella simulations before. What mdp parameters should I use to pull along the full box hight?

Thanks a lot Sebastian

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<div class="post-metadata">

**Author:** ![hess](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/hess/32/416_2.png) [@hess](https://gromacs.bioexcel.eu/u/hess)\
**Post date:** [September 28, 2022, 11:38am UTC](https://gromacs.bioexcel.eu/t/awh-sampling-across-periodic-boundaries/4876/4 "2022-09-28T11:38:33Z")

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I assume that you use the membrane as a reference with cylinder pulling. In that case I would think you can pull to nearly half the box height both up and down from the center of the membrane. I must say that I have not tested this myself.