Hi John, Welcome to VOTCA user group.
I understand your coarse-graining problem as follows. You have a reference atomic system containing your research molecule. Then you choose a mapping scheme such that the coarse-grained beads in a CG molecule have charges on them and now you want to determine a CG non-bonded interactions between these CG beads. So, in this case you can model your CG force field such that there are two types of interactions between the CG beads: non-Coulombic short-range CG potential + long-range Coulombic interactions. For the long-range Coulomb forces you can use the methods such as PME and the non-Coulombic short-range CG potential can be determined by one of the CG methods in VOTCA. For example, assuming you are using GROMACS, to use the described CG force field, the .mdp file options should be . . . coulombtype = pme vdw-type = User . . . and the rest you can follow from the tutorials. I hope above suggestion helps. Best, Sikandar On Wed, Dec 30, 2015 at 10:18 AM, John Voorehes <[email protected]> wrote: > I am a new to the VOTCA package. I want to use this package for the > coarse-graining simulation of my research molecule. Unlike the tutorial > molecules, the beads for my molecule has charges. So, my question is, does > the non-bonded interactions between two beads include Coulombic > interactions too or is it just LJ potential/VDW? Are there any ways I can > have coulombic interaction only? > > -- > 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 post to this group, send email to [email protected]. > Visit this group at https://groups.google.com/group/votca. > For more options, visit https://groups.google.com/d/optout. > -- 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 post to this group, send email to [email protected]. Visit this group at https://groups.google.com/group/votca. For more options, visit https://groups.google.com/d/optout.
