To address this, we have included following code in the .mdp file of minimization, equilibration and production of gromacs files.
define = -DDUMY_POS_RES
We tried three different options.
(i) with pressure coupling
(ii) with freeze grps
(iii) without pressure coupling
Mary Pitman
Is there a reason you can't use the same position restraint method for the system as the all-atom protocol form the BUMPy reference manuscript? Look back over their section on their all-atom protocol.
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