Is there any guideline for that?
My exact question is about topology file for using tabulated potential. What should be the statement mentioning nbfunc ( and combination-rule) in .top file when I wanted to have both potential (LJ and BKS)? Best, Narjes Narjes Khosravian Postdoc Researcher Department of Physics, Materials and Surface Theory Chalmers University of Technology SE-412 96 Göteborg, Sweden ________________________________ From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Mark Abraham <mark.j.abra...@gmail.com> Sent: Thursday, June 8, 2017 10:38:01 AM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Lennard Jones and Buckingham potential together in one simulation Hi, Isn't this covered in those PDFs? Mark On Thu, Jun 8, 2017 at 10:34 AM Narjes Khosravian < narjes.khosrav...@chalmers.se> wrote: > Hi Mark, > > Thanks for your reply! > > Actually I am using tabulated-potential based on the bellow manual by > Gareth Tribello. > <http://www.gromacs.org/@api/deki/files/94/=gromacs_nb.pdf> > > <http://www.gromacs.org/@api/deki/files/94/=gromacs_nb.pdf> > http://www.gromacs.org/@api/deki/files/94/=gromacs_nb.pdf > > My problem is that: > > Since I have LJ and buckingham both, what should be the statement > mentioning nbfunc ( and combination-rule) in .top file? e.g. nbfunc=1 > followed by LJ parameters C and A for the concerned pairs and > > then nbfunc=2 (and whatever combination rule) , followed by buckingham > parameters C, A , B for concerned pairs in the .top file? > > I greatly appreciate for any help in this matter. > Best, > Narjes > > > > ________________________________ > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se < > gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Mark > Abraham <mark.j.abra...@gmail.com> > Sent: Thursday, May 4, 2017 3:49:26 PM > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] Lennard Jones and Buckingham potential together > in one simulation > > Hi, > > This procedure is usually motivated by trying to mix force fields that were > never intended to be used together, and thus need to be shown work well > together. In that case, you may as well parameterize a consistent model. > > Technically, you might be able to get this to work, but each atom in > GROMACS can have only one set of VDW parameters, so you need to make the > same parameters work with both functional forms, and this either impossible > or tricky. The best bet is using tabulated interactions. Don't try to set > up your intended target simulation in your first attempt - make something > simple that lets you prove to yourself you have the interactions working > the way that you think they should, then add complexity. > > Mark > > On Wed, May 3, 2017 at 8:41 PM Narjes Khosravian < > narjes.khosrav...@chalmers.se> wrote: > > > Dear gromacs users, > > > > > > I am trying to use Lennard Jones and Buckingham potential together in > > one simulation as part of my system is treated by LJ and rest by Buck > > potential. > > > > > > My question is that how I can include Lennard Jones parameters in > topology > > file while my [defaults ] was chosen 2 1 to consider Buckingham > parameter? > > > > I have created table for buck and LJ. > > > > > > I greatly appreciate for any guide in this matter. > > > > Narjes > > > > > > Narjes Khosravian > > Postdoc Researcher > > Department of Physics, Materials and Surface Theory > > Chalmers University of Technology > > SE-412 96 Göteborg, Sweden > > > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to gmx-users-requ...@gromacs.org. > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.