Hi , Thank you very much .I will take all these factors in to account while building the model.
Thank you, Mohan. On Thu, Aug 30, 2012 at 5:53 PM, Mark Abraham <mark.abra...@anu.edu.au> wrote: > On 30/08/2012 10:17 PM, Mark Abraham wrote: >> >> On 30/08/2012 10:02 PM, mohan maruthi sena wrote: >>> >>> Hi, >>> I am going through it , i will understand it and try to build >>> the topology. >> >> >> Fundamentally, harmonic bonds do not serve your purpose, since you need an >> interaction that is harmonic in the change in distance, not harmonic in the >> distance. Hence your problems with collapsing systems. As such, you want to >> look at using distance restraints, rather than [bonds]. > > > On second thoughts, a sufficient network of harmonic bonds can suffice, but > you need to embed the distance in the topology. [distance_restraints] are > just easier because you can let the initial structure determine the > equilibrium position. (Unless you don't want that) > > Mark > > >> >> Mark >> >>> Thank you, >>> Mohan >>> >>> On Thu, Aug 30, 2012 at 5:12 PM, Tsjerk Wassenaar <tsje...@gmail.com> >>> wrote: >>>> >>>> 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 >> >> > > -- > 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