# Ubrella sampling

**URL:** <https://gromacs.bioexcel.eu/t/ubrella-sampling/10236>\
**Category:** User discussions\
**Created:** [September 26, 2024, 9:13am UTC](https://gromacs.bioexcel.eu/t/ubrella-sampling/10236 "2024-09-26T09:13:30Z")\
**Posts on this page:** 1\
**Page:** 1

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**Author:** ![Deme](https://avatars.discourse-cdn.com/v4/letter/d/7993a0/32.png) [@Deme](https://gromacs.bioexcel.eu/u/Deme)\
**Post date:** [September 26, 2024, 9:13am UTC](https://gromacs.bioexcel.eu/t/ubrella-sampling/10236/1 "2024-09-26T09:13:30Z")

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Dear all,  
I hope you are doing well,  
I want to potential of mean force (PME) using the umbrella sampling  
algorithm as one methane molecule is dragged following one straight line along the z direction  
of the simulation box. My simulation box looks as follows.  
How can I set umbrella sampling setting ? Could any one help me please?  
; Pull code  
pull = yes  
pull\_ncoords = 1 ; only one reaction coordinate  
pull\_ngroups = 2 ; two groups defining one reaction coordinate  
pull\_group1\_name =  
pull\_group2\_name =  
pull\_coord1\_type = umbrella ; harmonic potential  
pull\_coord1\_geometry = distance ; simple distance increase  
pull\_coord1\_dim = N N Y  
pull\_coord1\_groups = 1 2  
pull\_coord1\_start = yes ; define initial COM distance \> 0  
pull\_coord1\_rate = 0.01 ; 0.01 nm per ps = 10 nm per ns  
pull\_coord1\_k = 1000 ; kJ mol^-1 nm^-2

 ![Screenshot from 2024-09-26 17-10-54](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/2X/7/7c5a692e78e966b8d8c6d06345a2cbcf30fa9845.jpeg)

Deme

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