I have VOTCa already installed. Thank you for this. Steven
On Wed, Feb 13, 2013 at 10:34 PM, Broadbent, Richard <[email protected]> wrote: > Dear Steven, > > There is no universal method to do this and many people spend years > studying the various techniques. However, > http://pubs.acs.org/doi/abs/10.1021/ct900369w gives an overview of some of > the most widespread techniques used and its references will provide > further details. Futhermore, the VOTCA code it describes (www.votca.org) > provides tools for building such potentials and is compatible with gromacs > file formats. > > Regards, > > Richard > > On 13/02/2013 16:07, "Steven Neumann" <[email protected]> wrote: > >>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? >> >>Thank you >> >>Steven >>-- >>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 > > -- > 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 -- 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
