# PMF of a small molecule across a slab that has vapor-liquid interface

**URL:** <https://gromacs.bioexcel.eu/t/pmf-of-a-small-molecule-across-a-slab-that-has-vapor-liquid-interface/7046>\
**Category:** User discussions\
**Tags:** mdp-parameters, awh, umbrella-sampling, pull-code\
**Created:** [August 20, 2023, 7:21am UTC](https://gromacs.bioexcel.eu/t/pmf-of-a-small-molecule-across-a-slab-that-has-vapor-liquid-interface/7046 "2023-08-20T07:21:24Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![sptiwari](https://avatars.discourse-cdn.com/v4/letter/s/258eb7/32.png) [@sptiwari](https://gromacs.bioexcel.eu/u/sptiwari)\
**Post date:** [August 20, 2023, 7:21am UTC](https://gromacs.bioexcel.eu/t/pmf-of-a-small-molecule-across-a-slab-that-has-vapor-liquid-interface/7046/1 "2023-08-20T07:21:24Z")

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GROMACS version:  
GROMACS modification: No

Dear users,

Consider the setup of a simulation box shown in attached image file. Box contains vapor-liquid interface, and consists of water and monoethanolamine (a small molecule) molecules. PBC is applied in all three directions.

 ![box_and_rough_PMF](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/2X/9/92beaaf1b699fe32580e2383ee2112e79b3ee58a.png)

I wish to move a monoethanolamine molecule (let’s call it my\_MEA) across the box along the Z-axis and plot the potential mean force (PMF), which will look something as shown in the attached figure. Can anyone kindly provide an MDP file for doing this.

Additionally, I wish to do this using both umbrella sampling and AWH methods. Two MDP files for both the methods will be great.

In particular, I am confused about the following options:

1. pull-coord1-geometry: should I use distance or direction or direction-periodic.
2. pull-group1-pbcatom: Should I use -1 to turn on the cosine weighting.
3. Can I use pull\_group1\_name = System, and pull\_group2\_name = my\_MEA.

After reading the manual and related articles, I have come up with the following options. Can someone please verify if these options are correct.

```auto
; Pull code
pull = yes
pull_ncoords = 1 ; only one reaction coordinate
pull_ngroups = 2 ; two groups defining one reaction coordinate
pull-group1-pbcatom = -1 ; -1 means turn on the cosine weighting
pull_group1_name = System
pull_group2_name = my_MEA
pull_coord1_geometry = distance ; simple distance increase
pull_coord1_dim = N N Y
pull_coord1_groups = 1 2

pull_coord1_start = no

pull-coord1-type = external-potential ;umbrella
pull-coord1-potential-provider = awh

awh = yes
awh-nbias = 1
awh1-ndim = 1
awh1-dim1-coord-index = 1
;5.49102 5.49102 16.47306
awh1-dim1-start = 0
awh1-dim1-end = 3.5
awh1-dim1-force-constant = 12800
awh1-dim1-diffusion = 5e-5
awh1-error-init = 10

awh-share-multisim = yes
awh1-share-group = 1
awh1-equilibrate-histogram = yes

awh-nstout = 40000

```

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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:** [August 21, 2023, 6:28am UTC](https://gromacs.bioexcel.eu/t/pmf-of-a-small-molecule-across-a-slab-that-has-vapor-liquid-interface/7046/2 "2023-08-21T06:28:04Z")

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You should use geometry=direction. I would suggest using cosine weighting.

You’re other options look reasonable, but I only had a quick look.