Thanks Justin I have any question?
i will use minimization with this restrain. using genrestr I make min.itp. how should I use this .itp file in grompp or mdrun? On Fri, Feb 22, 2013 at 2:41 AM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 2/21/13 6:09 PM, Mehdi Bagherpour wrote: > >> I am using Gromacs software for DNA simulation. Specially in my project I >> need to fix two ends base pairs of DNA,The DNA that I want to simulate has >> 12 sequence shown bellow >> >> 5-- *C*GCAAAAAACG*C* --3 >> 3-- *G*CGTTTTTTGC*G* --5 >> >> >> I dont know how I can use from position restraint in gromacs. >> >> would you please help me to solve this problem? >> >> > Use genrestr with an index group specifying whatever it is that you want > to restrain. > > -Justin > > -- > ==============================**========== > > Justin A. Lemkul, Ph.D. > Research Scientist > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> > > ==============================**========== > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > * Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<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<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
