# Umbrella sampling opposite pull

**URL:** <https://gromacs.bioexcel.eu/t/umbrella-sampling-opposite-pull/8511>\
**Category:** User discussions\
**Created:** [March 5, 2024, 11:53am UTC](https://gromacs.bioexcel.eu/t/umbrella-sampling-opposite-pull/8511 "2024-03-05T11:53:14Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![mayank](https://avatars.discourse-cdn.com/v4/letter/m/bc8723/32.png) [@mayank](https://gromacs.bioexcel.eu/u/mayank)\
**Post date:** [March 5, 2024, 11:53am UTC](https://gromacs.bioexcel.eu/t/umbrella-sampling-opposite-pull/8511/1 "2024-03-05T11:53:14Z")

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Hi,

I have been performing Umbrella Sampling simulations. Regarding the stage of the steered molecular dynamics simulation, I would like to know how to pull a group along the z coordinate in the opposite direction.

I have two ligands for one I am able to pull out in the correct direction. But for the other ligand it is going in the opposite direction.

this is the mdp file

pull = yes  
pull\_ncoords = 1 ; only one reaction coordinate  
pull\_ngroups = 2 ; two groups defining one reaction coordinate  
pull\_group1\_name = LIG  
pull\_group2\_name = pocket  
pull\_coord1\_type = umbrella ; harmonic potential  
pull\_coord1\_geometry = distance ; simple distance increase  
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\_coord1\_rate = 0.01 ; 0.01 nm per ps = 10 nm per ns  
pull\_coord1\_k = 1000 ; kJ mol^-1 nm^-2

Sincerely,

Mayank

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<div class="post-metadata">

**Author:** ![obZehn](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/obzehn/32/2629_2.png) [@obZehn](https://gromacs.bioexcel.eu/u/obZehn)\
**Post date:** [March 5, 2024, 12:55pm UTC](https://gromacs.bioexcel.eu/t/umbrella-sampling-opposite-pull/8511/2 "2024-03-05T12:55:38Z")

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What do you mean specifically? I think what the pull code does is to just increase the distance (with the distance geometry) between two groups, that is, one group will be pushed in one direction and the other group in the other opposite direction.

If you mean how you want now to pull in the other direction, i.e., having the groups come together, then you have to invert the velocities. You are using the distance as type of pulling geometry (pull\_coord1\_geometry = distance) which requires the definition of the dimensions along which you are pulling (you set pull\_coord1\_dim = N N Y, so I guess you want to pull along z). In theory the definition of the vector (this line in your mdp file pull\_coord1\_vec = 0 0 -1) is useless here, as the geometry distance will read only the pull\_coord1\_dim value ([here](https://manual.gromacs.org/documentation/current/user-guide/mdp-options.html#mdp-value-pull-coord1-geometry-distance) in the manual is well documented). If you want the distance of the groups to decrease then you have to set a negative velocity, in your case pull\_coord1\_rate = -0.01.