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1

GROMACS version:2023.1
GROMACS modification: No

Hello,

My goal is to gradually pull group1 away from group2, where group3 and group4 are both residues belonging to group1, so that the relative orientation should be fixed (Is this pulling method reasonable?).

Here is my pulling setting:

pull = yes
pull_ncoords = 1
pull_ngroups = 4
pull-group1-name = PULLED
pull-group2-name = FIXED
pull-group3-name = ARG442
pull-group4-name = LYS417
pull-coord1-type = umbrella
pull-coord1-geometry = direction-relative
pull-coord1-groups = 1 2 3 4
pull-coord1-vec = 4 3
pull-coord1-rate = 0.005 ; nm/ps
pull-coord1-start = yes
pull_coord1-k = 1000
pull-group1-pbcatom = 8050
pull-group2-pbcatom = 32023
pull-pbc-ref-prev-step-com = yes

I met such error:

Program:     gmx grompp, version 2023.1
Source file: src/gromacs/gmxpreprocess/readpull.cpp (line 72)

Fatal error:
Expected three numbers at input line 4 3

For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors

I have no idea which parameter is going wrong.

Best wishes,
Wentao

2

If you’re using pull-coord1-geometry = direction-relative, then there’s no need to specify pull-coord1-vec because, according to the documentation,

the pull vector is the vector that points from the COM of a third to the COM of a fourth pull group. This means that 4 groups need to be supplied in pull-coord1-groups.

pull-coord1-vec always expects 3 values because these are the x, y, z components of the pulling vector, but in this case the vector is specified by the selection in pull-coord1-groups.

3

Thank you very much! I understand it.