Another Problem with Distances Between Pull Groups

User discussions
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1

GROMACS version: 2021.3
GROMACS modification: No

Hi all,

I am attempting to tether multiple proteins to a lipid bilayer using the following pull code:

; Pull Code
pull = yes
pull-print-com = yes
pull_ngroups = 32
pull-ncoords = 16

pull-coord1-groups= 1 2
pull_group1_name = PROA
pull_group2_name = LIPA
pull-coord1-type = umbrella
pull-coord1-geometry = distance
pull-coord1-dim = Y Y Y
pull-coord1-start = no
pull-coord1-rate = 0
pull-coord1-k= 10000

but getting this following error:

Fatal error:
Distance between pull groups 1 and 2 (8.370350 nm) is larger than 0.49 times
the box size (7.643079).

Even though the distance when visualized is ~0.1nm. Neither of the pull groups are located along the periodic boundary, but it seems that gromacs is calculating distances using one of the periodic image instead of the closest. This seems to echo this older issue, but the suggested solutions are not working in this case.

I appreciate any advice on how to handle this error. I have tried picking other lipids which are further from the protein group, but this is more of a bandaid with no insight on how to choose a minimum distance.

2

There are several issues in the mdp parameter you show here, but these can’t be correct. You can’t use two groups with the same name. And do you really want to control the distance along all three dimensions?

If you only want the molecules to be close to the membrane along z, you should use a single group for the whole membrane ad use cylinder geometry.

3

I only posted the relevant portion of the mdp, if that’s the error you’re referring to? There was also a typo in the original post (now corrected).
I do want to control the distance in all three dimensions and only between a single lipid and a protein, so that the protein and lipid are diffusing together. This is the same method I’ve used for other systems, so I do not understand why the error is occuring now.

4

hello, could you solve the problem? i have got the same error