This is the error message :
ERROR 1 [file 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 1 is larger than that and does not have a specific atom selected as reference atom.
Pull group natoms pbc atom distance at start reference at t=0
1 9518 4759
2 2993 11015 4.661 nm 4.661 nm
Estimate for the relative computational load of the PME mesh part: 0.18This run will generate roughly 1924 Mb of datawriting run input file...
I have also attached the mdp file.
I am following Justin Lemkul's Umbrella Sampling tutorial.
Dear Agnivo Gosai
This means that group 1 is very large and some atoms in that group are distant from each other more than 0.5 times the box size. This is a problem for GROMACS when it tries to calculate distances, since PBC are on and the true distance is not well defined anymore.
Try to visualize group 1 with some tool like VMD and try to find an atom that is ca. at the centre of your group 1. Take that atom number from the .gro/.pdb/your structure file and then add the option
pull-group1-pbcatom = #number_of_your_central_atom
to your mdp file (https://manual.gromacs.org/documentation/2018/user-guide/mdp-options.html#com-pulling).
When you do not specify this option, gromacs just searches for the central atom in the group from the list, i.e., if you have a group of 10 atoms gromacs uses the fifth, which does not correspond necessarily with the geometrical centre of your group. This usually is not a problem, but when groups are larger than half the box then the choice could be not ideal to calculate distances with PBC, and so you have to specify a better atom for gromacs to use.
Hope this helps,
Nicola
Thank you Nicola for your highly beneficial answer which helped a ton.
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