Tanks Justin Should I use from 'define = -DPOSRES' in mdp file?
On Fri, Feb 22, 2013 at 4:13 AM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 2/21/13 7:35 PM, Mehdi Bagherpour wrote: > >> 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? >> >> >> > As you would any other .itp file; #include it in the topology, within the > corresponding [moleculetype]. > > -Justin > > >> 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://vt.edu/Pages/Personal/justin> >>> <h**ttp://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> >>> <htt**p://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<h**ttp://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> >>> <http://**www.gromacs.org/Support/**Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> >>> > >>> >>> > -- > ==============================**========== > > 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
