# Umbrella Sampling: Currently all umbrella pull coordinates should operate on the same dimensions **URL:** \ **Category:** User discussions\ **Created:** [October 16, 2020, 2:45pm UTC](https://gromacs.bioexcel.eu/t/umbrella-sampling-currently-all-umbrella-pull-coordinates-should-operate-on-the-same-dimensions/970 "2020-10-16T14:45:22Z")\ **Posts on this page:** 7\ **Page:** 1
**Author:** ![amit7urmc](https://avatars.discourse-cdn.com/v4/letter/a/b5e925/32.png) [@amit7urmc](https://gromacs.bioexcel.eu/u/amit7urmc)\ **Post date:** [October 16, 2020, 2:45pm UTC](https://gromacs.bioexcel.eu/t/umbrella-sampling-currently-all-umbrella-pull-coordinates-should-operate-on-the-same-dimensions/970/1 "2020-10-16T14:45:22Z")
GROMACS version: 5.1.4 GROMACS modification: Yes/No Hello everybody, I ran Umbrella simulations, largely guided by tutorial as [here](http://www.mdtutorials.com/gmx/umbrella/07_analysis.html) and then I tweaked few parameters in the mdp file …based on my understanding. Post pulling simulation, I used 0.1nm separation window and ran 24 simulations each lasting for 2.5ns. At the end I prepared a list of .tpr and pullf.xvg in separate .dat files and I gave the command. “gmx\_mpi wham -it tpr-files.dat -if pullf-files.dat -o -hist -unit kCal”. Immediately an error is raised **Fatal error:** **Currently all umbrella pull coordinates should operate on the same dimensions** I have two pull co-ordinates and I am pasting the details of the md\_pull.mdp and md\_umbrella.mdp below. ========================== **md\_pull.mdp** ; Pull code pull = yes pull\_ncoords = 2 ; only one reaction coordinate pull\_ngroups = 2 ; two groups defining one reaction coordinate pull\_group1\_name = Restrained\_Protein pull\_group2\_name = Moving\_LIG pull-group1-pbcatom = 1794 pull-group2-pbcatom = 2976 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 = 0.0075 ; 0.01 nm per ps = 10 nm per ns pull\_coord1\_k = 250 ; kJ mol^-1 nm^-2 pull\_coord2\_type = umbrella ; harmonic potential pull\_coord2\_geometry = distance ; simple distance increase pull\_coord2\_dim = N Y N pull\_coord2\_groups = 1 2 pull\_coord2\_start = yes ; define initial COM distance \> 0 pull\_coord2\_rate = 0.0075 ; 0.01 nm per ps = 10 nm per ns pull\_coord2\_k = 250 ; kJ mol^-1 nm^-2 ================================= and **md\_umbrella.mdp** ; Pull code pull = yes pull\_ncoords = 2 ; only one reaction coordinate pull\_ngroups = 2 ; two groups defining one reaction coordinate pull\_group1\_name = Restrained\_Protein pull\_group2\_name = Moving\_LIG pull-group1-pbcatom = 1794 pull-group2-pbcatom = 2976 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 = 0.0 ; 0.01 nm per ps = 10 nm per ns pull\_coord1\_k = 250 ; kJ mol^-1 nm^-2 pull\_coord2\_type = umbrella ; harmonic potential pull\_coord2\_geometry = distance ; simple distance increase pull\_coord2\_dim = N Y N pull\_coord2\_groups = 1 2 pull\_coord2\_start = yes ; define initial COM distance \> 0 pull\_coord2\_rate = 0.0 ; 0.01 nm per ps = 10 nm per ns pull\_coord2\_k = 250 ; kJ mol^-1 nm^-2 - Looks like the tweaks I did to the mdp file were not correct. What mistake(s) I did that resulted in this error? - Is there a way to get around the problem now or I have to restart again with …something parameters changed? Thank you very much in anticipation. Amit ---
**Author:** ![alevilla](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/alevilla/32/439_2.png) [@alevilla](https://gromacs.bioexcel.eu/u/alevilla)\ **Post date:** [October 19, 2020, 4:44pm UTC](https://gromacs.bioexcel.eu/t/umbrella-sampling-currently-all-umbrella-pull-coordinates-should-operate-on-the-same-dimensions/970/2 "2020-10-19T16:44:56Z")
Hi, gmx wham requires for multi coordinates that the pull coordinates operate on the same dimensions. In alternative you can analyze one coordinate (see [http://manual.gromacs.org/current/onlinehelp/gmx-wham.html?highlight=gmx%20wham](http://manual.gromacs.org/current/onlinehelp/gmx-wham.html?highlight=gmx%20wham)) Best regards Alessandra ---
**Author:** ![amit7urmc](https://avatars.discourse-cdn.com/v4/letter/a/b5e925/32.png) [@amit7urmc](https://gromacs.bioexcel.eu/u/amit7urmc)\ **Post date:** [October 20, 2020, 8:13am UTC](https://gromacs.bioexcel.eu/t/umbrella-sampling-currently-all-umbrella-pull-coordinates-should-operate-on-the-same-dimensions/970/3 "2020-10-20T08:13:05Z")
@alevilla Thank you very much. If I understand correctly, I am supposed to use “-is coordsel.dat” as an option and in the coordsel.dat I have to write multiple lines of “1 0”? That way I use the first coordinate and ignore the second one. ---
**Author:** ![alevilla](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/alevilla/32/439_2.png) [@alevilla](https://gromacs.bioexcel.eu/u/alevilla)\ **Post date:** [October 20, 2020, 8:21am UTC](https://gromacs.bioexcel.eu/t/umbrella-sampling-currently-all-umbrella-pull-coordinates-should-operate-on-the-same-dimensions/970/4 "2020-10-20T08:21:47Z")
Yes, and the number of line in coordsel.dat should be equal to number of tpr files defined in tpr-files.dat. Kind regards Alessandra ---
**Author:** ![amit7urmc](https://avatars.discourse-cdn.com/v4/letter/a/b5e925/32.png) [@amit7urmc](https://gromacs.bioexcel.eu/u/amit7urmc)\ **Post date:** [October 20, 2020, 6:56pm UTC](https://gromacs.bioexcel.eu/t/umbrella-sampling-currently-all-umbrella-pull-coordinates-should-operate-on-the-same-dimensions/970/5 "2020-10-20T18:56:24Z")
@alevilla Thank you. But it gave the same error. ---
**Author:** ![alevilla](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/alevilla/32/439_2.png) [@alevilla](https://gromacs.bioexcel.eu/u/alevilla)\ **Post date:** [October 21, 2020, 7:28am UTC](https://gromacs.bioexcel.eu/t/umbrella-sampling-currently-all-umbrella-pull-coordinates-should-operate-on-the-same-dimensions/970/6 "2020-10-21T07:28:35Z")
Hi, hmm, sorry, I could not find your specific error in the current source code. You can try the current version GROMACS 2020.4 or contact the authors for the tutorial you are following. kind regards Alessandra ---
**Author:** ![amit7urmc](https://avatars.discourse-cdn.com/v4/letter/a/b5e925/32.png) [@amit7urmc](https://gromacs.bioexcel.eu/u/amit7urmc)\ **Post date:** [October 22, 2020, 4:52am UTC](https://gromacs.bioexcel.eu/t/umbrella-sampling-currently-all-umbrella-pull-coordinates-should-operate-on-the-same-dimensions/970/7 "2020-10-22T04:52:50Z")
@alevilla Thank you for looking into the source code. I really appreciate it.