<html><head><meta http-equiv=Content-Type content="text/html; charset=utf-8"><META name="Author" content="Novell GroupWise WebAccess"></head><body style='font-family: Helvetica, Arial, sans-serif; font-size: 13px; '>Hi Thomas,<br><br>Wouldn't it be an idea to smooth this tabulated potential within some range<br>down to zero (1.0-1.4). One could use a simple single-exponential decay in<br>a switch-function manner. Just one suggestion and maybe not your solution.<br><br>Bests,<br><br>Emanuel<br><br>>>> Thomas Schlesier <schlesi@uni-mainz.de> 13.01.12 14.29 Uhr >>><br>Dear all,<br>first of all, sorry to this rather conceptional question, which is not <br>totally to GROMOACS related. But probably anyone of you can help.<br><br>In my simulations I use mesitylene as a solvent. In future i want to <br>coarse-grain the full atomic mesitylene to an effective one-particle. <br>For this i did a NPT-simulation to obtain the RDF (with regard to the <br>COM of the molecules) from which i want to calculate an effective <br>interaction potential by iterative boltzmann. The full-atomistic <br>simulations (slovate + solvent) employed a cut-off of 1.4 nm.<br>At this distance (1.4 nm) the RDF shows it second minimum (RDF=0.97) and <br>after 1.8 nm the RDF is around 1.0 +/- 0.15 (I got the RDF only up to a <br>distance of 2.3 nm).<br>Now my question is how long should be the table for the effective <br>potential (i.e. maximum distance for an interaction)? If i would use 1.4 <br>nm, i would have a jump in the interaction potential (which is normal <br>due to the truncation of the cut-off). But for coulomb-interaction one <br>would have PME or other stuff which would correct the artifects to some <br>degree.<br>Or would it be better to use a long interaction table (interactions at <br>longer distances) and truncate the table at a distance after 1.4 nm <br>where the RDF is equal to 1?<br><br>Hope anybody can give some insight.<br><br>Greetings<br>Thomas<br>-- <br>gmx-users mailing list gmx-users@gromacs.org<br>http://lists.gromacs.org/mailman/listinfo/gmx-users<br>Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!<br>Please don't post (un)subscribe requests to the list. Use the <br>www interface or send it to gmx-users-request@gromacs.org.<br>Can't post? Read http://www.gromacs.org/Support/Mailing_Lists<br><br></body></html>