Dear Christoph, Thank you for the clarification.
On Wednesday, February 22, 2023 at 10:09:06 AM UTC-5 Christoph Junghans wrote: > 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/498d2ac4-83ab-4212-82b4-09ebf1b2edd5n%40googlegroups.com.
