# Dependece of diffusion constant on force constant in AWH simulation

**URL:** <https://gromacs.bioexcel.eu/t/dependece-of-diffusion-constant-on-force-constant-in-awh-simulation/11455>\
**Category:** User discussions\
**Created:** [February 4, 2025, 6:49pm UTC](https://gromacs.bioexcel.eu/t/dependece-of-diffusion-constant-on-force-constant-in-awh-simulation/11455 "2025-02-04T18:49:44Z")\
**Posts on this page:** 5\
**Page:** 1

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**Author:** ![mjianming](https://avatars.discourse-cdn.com/v4/letter/m/2bfe46/32.png) [@mjianming](https://gromacs.bioexcel.eu/u/mjianming)\
**Post date:** [February 4, 2025, 6:49pm UTC](https://gromacs.bioexcel.eu/t/dependece-of-diffusion-constant-on-force-constant-in-awh-simulation/11455/1 "2025-02-04T18:49:44Z")

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GROMACS version: 2024.4  
GROMACS modification: No  
Hi,

I am simulating a particle permeating a membrane using the martini2 force field and wanted to compute the permeability of the membrane. To do this, I am using AWH to obtain the PMF and diffusion constant along Z.

While i was doing a test run on diffusion coefficient estimation in an isotrophic water box containing the solute particle, I found that the diffusion constant D\_z from the simulation is highly dependent on the chosen force constant of the potential. The D\_z decreases with increasing force constant. In my expectation, the estimation of D\_z should be relatively stable regardless of the choice of force constant.

Any comments or suggestions are appreciated.Thanks in advance for any help.

The attached is the results and the settings for the AWH simulation is as follows:  
pull = yes  
pull\_ncoords = 1 ; only one reaction coordinate  
pull\_ngroups = 2 ; two groups defining one reaction coordinate  
pull\_group1\_name = W  
;pull-group1-pbcatom = 1198  
;pull-group2-pbcatom = 12211  
;pull-pbc-ref-prev-step-com = yes  
pull\_group2\_name = EOL  
pull\_coord1\_type = external-potential  
pull-coord1-potential-provider = AWH  
pull\_coord1\_geometry = direction ; simple distance increase  
;pull-cylinder-r = 2  
pull\_coord1\_dim = N N Y  
pull\_coord1\_vec = 0 0 1  
pull\_coord1\_groups = 1 2  
pull\_coord1\_start = yes ; define initial COM distance \> 0  
pull-nstxout = 1000  
pull-nstfout = 0

awh = yes  
awh-nstout = 50000  
awh-nbias = 1  
awh-nstsample = 100  
awh-nsamples-update = 10  
awh-potential = convolved

awh1-ndim = 1  
awh1-dim1-coord-provider = pull  
awh1-dim1-coord-index = 1  
awh1-dim1-start = -2  
awh1-dim1-end = 0  
awh1-dim1-force-constant = 10000  
awh1-dim1-diffusion = 4e-3

 ![convolved](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/2X/e/e05b3acb7854d21b89c3c7dd3d0dba5ab806e7a8.png)

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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:** [February 7, 2025, 9:24am UTC](https://gromacs.bioexcel.eu/t/dependece-of-diffusion-constant-on-force-constant-in-awh-simulation/11455/2 "2025-02-07T09:24:14Z")

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Firstly, I recommend that you use geometry=cylinder. Now the whole membrane might deform, which can give artifacts in the PME and diffusion constant.

The diffusion constant will depend (strongly) on the force constant when the force constant is comparable to or smaller than the curvature of the free-energy landscape. So the question is what curvature you have. I would guess though that a force constant of 10000 should be sufficient, but there is still a strong change when going to 20000.

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<div class="post-metadata">

**Author:** ![mjianming](https://avatars.discourse-cdn.com/v4/letter/m/2bfe46/32.png) [@mjianming](https://gromacs.bioexcel.eu/u/mjianming)\
**Post date:** [February 7, 2025, 4:15pm UTC](https://gromacs.bioexcel.eu/t/dependece-of-diffusion-constant-on-force-constant-in-awh-simulation/11455/3 "2025-02-07T16:15:58Z")

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Thanks Hess for the detailed exaplanation. I will use the geometry=cylinder as you suggest for membrane systems.

The test systems and the above results are obtained in a simple anisotropic water box containing a solute without the membrane. The a Z span of ~ 1 nm is used for running AWH for the solute. The simulation quickly exit the initial stage and I did not run too long. Might it help if I run longer?

Thanks again.

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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:** [February 7, 2025, 4:30pm UTC](https://gromacs.bioexcel.eu/t/dependece-of-diffusion-constant-on-force-constant-in-awh-simulation/11455/4 "2025-02-07T16:30:21Z")

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But then you are measuring something very strange. I don’t understand what you are pulling against then.

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<div class="post-metadata">

**Author:** ![mjianming](https://avatars.discourse-cdn.com/v4/letter/m/2bfe46/32.png) [@mjianming](https://gromacs.bioexcel.eu/u/mjianming)\
**Post date:** [February 7, 2025, 4:36pm UTC](https://gromacs.bioexcel.eu/t/dependece-of-diffusion-constant-on-force-constant-in-awh-simulation/11455/5 "2025-02-07T16:36:28Z")

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Ah, I was pulling using an absolute coordinat, which may not be optimal. I also observed this dependence in a simulation with membrane. The solute in the bulk water (not interacting with membrane) has quite different D\_z when using different force constants. I’ll double check and thanks!