# AWH reaction coordinate

**URL:** <https://gromacs.bioexcel.eu/t/awh-reaction-coordinate/2482>\
**Category:** User discussions\
**Tags:** awh, pull-code\
**Created:** [July 9, 2021, 10:36am UTC](https://gromacs.bioexcel.eu/t/awh-reaction-coordinate/2482 "2021-07-09T10:36:20Z")\
**Posts on this page:** 3\
**Page:** 1

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**Author:** ![fabio](https://avatars.discourse-cdn.com/v4/letter/f/f4b2a3/32.png) [@fabio](https://gromacs.bioexcel.eu/u/fabio)\
**Post date:** [July 9, 2021, 10:36am UTC](https://gromacs.bioexcel.eu/t/awh-reaction-coordinate/2482/1 "2021-07-09T10:36:20Z")

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GROMACS version: 2018  
GROMACS modification: No

Hi all,  
I have a protein with two reacting groups. The distance between them observed in the x-ray structure is considered too long for that reaction to occur. So, a movement of the domains has been proposed to shorten that distance down to a widely accepted threshold.  
The distance between the two groups intuitively seems a good choice for a reaction coordinate to describe this hypothetical conformational change.  
I’m studying the AWH method, and I would like to use it to estimate the free energy of the process but it doesn’t allow me (with my settings) to bring two groups closer.  
When I feed grompp with the following mdp parameters

; PULL CODE  
pull = yes  
pull-ngroups = 2  
pull-group1-name = group1  
pull-group2-name = group2  
pull-ncoords = 1  
pull-coord1-type = external-potential  
pull-coord1-geometry = distance  
pull-coord1-groups = 1 2  
pull-coord1-potential-provider = awh

; AWH CODE  
awh = yes  
awh-potential = convolved  
awh-nbias = 1  
awh1-ndim = 1  
awh1-dim1-coord-index = 1  
awh1-dim1-start = 1.85  
awh1-dim1-end = 1.35  
awh1-dim1-force-constant = 150000  
awh1-dim1-diffusion = 5e-5  
awh1-error-init = 5  
awh-share-multisim = yes  
awh1-share-group = 1  
awh1-equilibrate-histogram = yes

it prints this:  
Fatal error:  
For the non-periodic pull coordinates awh1-dim1-start cannot be larger than  
awh1-dim1-end

Any suggestions on how to treat the R.C. geometry?

Many thanks in advance,

Fabio

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**Author:** ![gigo](https://avatars.discourse-cdn.com/v4/letter/g/74df32/32.png) [@gigo](https://gromacs.bioexcel.eu/u/gigo)\
**Post date:** [January 27, 2023, 1:13pm UTC](https://gromacs.bioexcel.eu/t/awh-reaction-coordinate/2482/2 "2023-01-27T13:13:57Z")

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Hello,  
I stumbled upon the same problem. I just can’t pull 2 groups towards one another in a non-periodic system, which makes use of awh impossible for some of my systems. Have you found a solution? Should we proceed with a bug report/feature request?  
Regards,  
g

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**Author:** ![MagnusL](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/magnusl/32/2380_2.png) [@MagnusL](https://gromacs.bioexcel.eu/u/MagnusL)\
**Post date:** [February 14, 2024, 12:15pm UTC](https://gromacs.bioexcel.eu/t/awh-reaction-coordinate/2482/4 "2024-02-14T12:15:18Z")

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Have you tried with `pull-geometry = direction` instead?