On Wed, Feb 22, 2023 at 7:03 AM Sanjeet Singh <[email protected]> wrote: > > Dear Christoph, > > Thank you for your reply. > > I have another query though. In the VOTCA tutorial for liquid hexane with FM > for non-bonded interactions only, it is mentioned that we have to exclude all > the intramolecular interactions also in addition to the all bonded > interaction. I am not getting why we need to exclude the intramolecular > nonbonded interaction also? Because, I think these interactions needs to be > accounted in the nonbonded interactions part.
The coarse-grained topology has #excl of 3 (https://github.com/votca/votca/blob/master/csg-tutorials/hexane/ibi_nonbonded/topol.top#L13) hence the A and B beads within a CG molecule don't interaction via non-bonded interaction and so are fully covered by the bonded interaction, which then means you need to exclude them for the non-bonded interaction calculation. I think this should be explained in more detail here: http://dx.doi.org/10.1002/mats.201100011 However the setup of #excl of 3 is a gromacs inspired, and you could certainly build a cg model where the A and B beads inside a molecule also interact via non-bonded interactions. This is more common when using lammps though. Christoph > > Can you please clarify me on this. > > Thank you. > > Sanjeet > > On Monday, February 20, 2023 at 9:36:33 AM UTC-5 Christoph Junghans wrote: >> >> On Sat, Feb 18, 2023 at 8:26 PM Sanjeet Singh <[email protected]> wrote: >> > >> > Hello Everyone, >> > >> > I would like to derive the CG potential for a Homopolymer Electrolyte >> > system. But, I am confused that which approach among IBI, FM or REM would >> > be better. >> > >> > I know that IBI is not good for dilute system, considering the number of >> > ion pairs present in the system compared to the polymer. >> You are right, getting enough statistics for IBI in dilute systems can >> be cumbersome. I would try FM for the ions. >> And you can always combine it with an IBI potential for the polymer. >> >> Christoph >> >> > >> > Any suggestion would be of great help. >> > >> > Thank you. >> > >> > Sanjeet >> > >> > -- >> > Join us on Slack: https://join.slack.com/t/votca/signup >> > --- >> > You received this message because you are subscribed to the Google Groups >> > "votca" group. >> > To unsubscribe from this group and stop receiving emails from it, send an >> > email to [email protected]. >> > To view this discussion on the web visit >> > https://groups.google.com/d/msgid/votca/30253b43-c50e-45d3-8c3d-c39249452989n%40googlegroups.com. >> >> >> >> -- >> Christoph Junghans >> Web: http://www.compphys.de > > -- > Join us on Slack: https://join.slack.com/t/votca/signup > --- > You received this message because you are subscribed to the Google Groups > "votca" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to [email protected]. > To view this discussion on the web visit > https://groups.google.com/d/msgid/votca/56b684e7-8e04-4f49-8d74-e17dd24cfd73n%40googlegroups.com. -- Christoph Junghans Web: http://www.compphys.de -- Join us on Slack: https://join.slack.com/t/votca/signup --- You received this message because you are subscribed to the Google Groups "votca" group. To unsubscribe from this group and stop receiving emails from it, send an email to [email protected]. To view this discussion on the web visit https://groups.google.com/d/msgid/votca/CAHG27e5yeUmiv8RRp8tm0OCM-Vv4ch3D_FzQKW3UbTmq7CSO%3DQ%40mail.gmail.com.
