> Date: Wed, 13 Feb 2013 16:07:53 +0000 > From: Steven Neumann <[email protected]> > Subject: [gmx-users] Bond potential of atom groups > To: Discussion list for GROMACS users <[email protected]> > Message-ID: > <CAKZJqQEztzuGqm0t4=f37v+w-jioire0pz1tvdpj6cv7cyg...@mail.gmail.com> > Content-Type: text/plain; charset=ISO-8859-1 > > Dear Gmx Users, > > I want to create coarse grained model. I need bond constant and > equilibrium distance according to the equation > > V(r) =K (R - Req)^2 > > I wish to extract bonded potential between beads made out 3 atoms. I > need Req and K. Equilibrium distance is straight forward - g_dist > between COM or COG with index file conatining those 3 atoms. To match > force constant K I need to extract bonded potential and try to fit to > my parabolic curve. > > My question: > > How can I get bonded potential between beads of 3 atoms from AA > simulation? Do I have to specify energy groups (energgrps) before the > run in my mdp and then use g_energy? Have a look at the hexane example in the tutorials of the VOTCA package: <https://code.google.com/p/votca/source/browse/?repo=csg-tutorials#hg%2Fhexane%2Fatomistic> You will have to modify the mapping file (hexane.xml) a bit for your case, after that you can use the csg_boltzmann program to calculate the potential from the mapped distribution and try to fit the resulting potential table with the above mentioned functional form. (The VOTCA manual gives more details about these steps.)
If you have further questions contact the VOTCA mailing list: [email protected] Cheers, Christoph > > Thank you > > Steven -- Christoph Junghans Web: http://www.compphys.de -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
