Umbrella Sampling: Currently all umbrella pull coordinates should operate on the same dimensions

User discussions
1

GROMACS version: 5.1.4
GROMACS modification: Yes/No

Hello everybody,

I ran Umbrella simulations, largely guided by tutorial as here 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

2

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)
Best regards
Alessandra

3

@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.

4

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

5

@alevilla Thank you. But it gave the same error.

6

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

7

@alevilla Thank you for looking into the source code. I really appreciate it.