Hi Thomas, Wouldn't it be an idea to smooth this tabulated potential within some range down to zero (1.0-1.4). One could use a simple single-exponential decay in a switch-function manner. Just one suggestion and maybe not your solution.
Bests, Emanuel >>> Thomas Schlesier <schl...@uni-mainz.de> 13.01.12 14.29 Uhr >>> 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 -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
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