2016-01-04 8:39 GMT-07:00 John Voorehes <[email protected]>: > 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? No, for that you want to use coulombtype = PME-User which uses short-ranged table together with long-range part of PME.
Christoph > > 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]> 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. -- Christoph Junghans Web: http://www.compphys.de -- 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.
