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I am trying to do alchemical methods according to the following cycle (link below) to calculate the absolute binding free energy of a protein binding to DNA. However I get the following error whenever trying to do energy minimization
https://alchemistry.org/wiki/Absolute_Binding_Free_Energy_-_Gromacs_2016
Fatal error:
There are 1315162 perturbed, excluded non-bonded pair interactions beyond the
pair-list cut-off, which is not supported. This can happen because the system
is unstable or because intra-molecular interactions at long distances are
excluded. If the latter is the case, you can try to increase nstlist or rlist
to avoid this.The error is likely triggered by the use of couple-intramol=no
and the maximal distance in the decoupled molecule exceeding rlist.
I tried using a shorter DNA strand such that only the protein-contacting parts are included which makes the complex much smaller, but it gives the same error. From other similar posts I know that setting couple-intramol = yes will allow the minimization to run, however this requires an extra step in the alchemical cycle which most answers are very brief about. If someone could suggest a way to solve the minimization issue or give more info about this extra step (if using couple-intramol = yes) it would be greatly appreciated. I attached my minimization mdp.
enmin.00.mdp (2.3 KB)