Defining central atom in steered molecular dynamics

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1

GROMACS version:2021.1
GROMACS modification: No
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Hi,
How to select the central atom of a protein for pulling? if remain unselected following error is displayed,
[error 1(file MDP/md_pull.mdp)]
When the maximum distance from a pull group reference atom to other atoms in the group is larger than 0.5 times half the box size, a centrally placed atom should be chosen as pbcatom. Pull group 2 is larger than that & does not have a specific atom selected as reference atom.

Details about the system:
System size: 4.950 9.590 7.930
defined center: 3.0 5.5 4.0
Box size: 20 11 10
Pull-Dim: Y N N
pull_pbc_ref_prev_step_com = yes

Chain A: 50 residues
Chain B: 539 residues

Position restrain on Chain A
Pull rate: 0.001nm/ps
Force: 1000 kJ/mol

Please share your inputs to rectify the error.

Thanks
utk

2

Hi,

specify your central atom index with pull-group2-pbcatom = index in the .mdp file. More information here: Molecular dynamics parameters (.mdp options) — GROMACS 2021.2 documentation

Regards,
Petter

1 Like
3

Thanks petter, I was able to rectify the error.

Regards,
utk

4

Hi,
While performing further simulation at different pH, for system at higher pH and pull in X-axis no need to define the central atom but at lower pH the same complex in X-axis pull shows an error to define an central atom.
I am not able to understand this, Please help!
Thanks