Dear all,
first of all, sorry to this rather conceptional question, which is not totally to GROMOACS related. But probably anyone of you can help.

In my simulations I use mesitylene as a solvent. In future i want to coarse-grain the full atomic mesitylene to an effective one-particle. For this i did a NPT-simulation to obtain the RDF (with regard to the COM of the molecules) from which i want to calculate an effective interaction potential by iterative boltzmann. The full-atomistic simulations (slovate + solvent) employed a cut-off of 1.4 nm. At this distance (1.4 nm) the RDF shows it second minimum (RDF=0.97) and after 1.8 nm the RDF is around 1.0 +/- 0.15 (I got the RDF only up to a distance of 2.3 nm). Now my question is how long should be the table for the effective potential (i.e. maximum distance for an interaction)? If i would use 1.4 nm, i would have a jump in the interaction potential (which is normal due to the truncation of the cut-off). But for coulomb-interaction one would have PME or other stuff which would correct the artifects to some degree. Or would it be better to use a long interaction table (interactions at longer distances) and truncate the table at a distance after 1.4 nm where the RDF is equal to 1?

Hope anybody can give some insight.

Greetings
Thomas
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