Thank you very much, Sikandar. Right now, we are only focusing on the short range coulombic interactions in a specified cutoff radius. In order to calculate the interaction can I define the coulombtype as User / does PME work for SR Coulombic interactions also?
On Wednesday, December 30, 2015 at 10:31:08 PM UTC-6, sikandar wrote: > > 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] > <javascript:>> 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] <javascript:>. >> To post to this group, send email to [email protected] <javascript:> >> . >> 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.
