Hi Mohan, You need to check chapter 5 of the gromacs manual to understand the topology format to write. You probably need only to define one atom type and the C6/C12 parameters could probably even be set to zero. You need to write an [ atoms ] section, and a [ bonds ] section, according to the specifications in the manual.
Cheers, Tsjerk On Thu, Aug 30, 2012 at 1:32 PM, mohan maruthi sena <maruthi.s...@gmail.com> wrote: > Hi, > Thanks for a quick reply. In these models we use a distance > cut-off method. Around a particular atom we take a cut-off distance > and connect to all those atoms which fall in the cut-off. I do not > understand, how to connect this atoms with the other atoms falling in > cut-off distance. I have written a script to know the atom numbers > falling with in cut-off distance. I replace bonds section in topology > with these atom connectivity information that i got from script. Is > this method correct or else please suggest me a way.Can you elaborate > on "write a script to generate .top" > > > Thank you very much, > Mohan > > On Thu, Aug 30, 2012 at 3:18 PM, Tsjerk Wassenaar <tsje...@gmail.com> wrote: >> Hi Mohan, >> >> Elastic network modeling consists of building a Hessian matrix based >> on the distances. That matrix is then diagonalized and the modes are >> further investigated. You could write a script to generate a .top file >> with a [ bonds ] section, capturing the elastic bonds, and then use >> Gromacs to generate the Hessian using the nm integrator. But that >> seems more trouble than it's worth. If you think of building such a >> model and then simulate it using an md integrator, be warned that >> these models are very incomplete and are intended to only capture the >> tangents around the starting structure. >> >> Hope it helps, >> >> Tsjerk >> >> On Thu, Aug 30, 2012 at 9:22 AM, mohan maruthi sena >> <maruthi.s...@gmail.com> wrote: >>> Hi all, >>> Can any one suggest me how to build elastic network model >>> in gromacs. >>> >>> >>> >>> >>> Thanks, >>> Mohan >>> -- >>> gmx-users mailing list gmx-users@gromacs.org >>> 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 gmx-users-requ...@gromacs.org. >>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> >> >> -- >> Tsjerk A. Wassenaar, Ph.D. >> >> post-doctoral researcher >> Molecular Dynamics Group >> * Groningen Institute for Biomolecular Research and Biotechnology >> * Zernike Institute for Advanced Materials >> University of Groningen >> The Netherlands >> -- >> gmx-users mailing list gmx-users@gromacs.org >> 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 gmx-users-requ...@gromacs.org. >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- > gmx-users mailing list gmx-users@gromacs.org > 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 gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- gmx-users mailing list gmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
