Well my first question is: if the pdb2gmx command must take a force file? I guess it should be necessary. Then the available list contains amber and others, but not user-specified potential. This will affect the future simulation or calculation?
On Thu, Nov 17, 2011 at 10:06 AM, Justin A. Lemkul <[email protected]> wrote: > > > Liu, Liang wrote: > >> Well, I already have the xvg files from others. However I don't know how >> to use it. >> >> > Start with the manual, where modifications to the topology and relevant > commands and files are described. Then refer to the how-to online, which > has specific instructions. Then, ask specific questions of problems you > are having. I doubt anyone on this list will be able or willing to guess > where your problems are at this point. > > -Justin > > On Thu, Nov 17, 2011 at 10:00 AM, Justin A. Lemkul <[email protected]<mailto: >> [email protected]>> wrote: >> >> >> >> Liu, Liang wrote: >> >> Dear all, >> >> I am trying to calculate potentials for RNA structures with a >> serial of tabulated potentials (non-bonded). >> And the only potential I am going to use is the tabulated >> potentials, and the effect from force field should be removed. >> However, when I use pdb2gmx to build the topology file, I have >> to choose a force field. What should I do for that? Thanks. >> >> >> It sounds like you need to be constructing your own force field, >> completely, from scratch. If you're not looking to use the existing >> force fields, this sounds like the only real solution. You can take >> the time to make .xvg files for bonded and nonbonded interactions >> (see the manual), but that is probably just as much work and your >> simulations will be much slower. >> >> -Justin >> >> -- ==============================**__========== >> >> >> Justin A. Lemkul >> Ph.D. Candidate >> ICTAS Doctoral Scholar >> MILES-IGERT Trainee >> Department of Biochemistry >> Virginia Tech >> Blacksburg, VA >> jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080 >> <tel:%28540%29%20231-9080> >> >> http://www.bevanlab.biochem.__**vt.edu/Pages/Personal/justin<http://vt.edu/Pages/Personal/justin> >> >> <http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> >> > >> >> ==============================**__========== >> >> -- gmx-users mailing list [email protected] >> <mailto:[email protected]> >> >> http://lists.gromacs.org/__**mailman/listinfo/gmx-users<http://lists.gromacs.org/__mailman/listinfo/gmx-users> >> >> >> <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> >> >> >> <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 [email protected] >> <mailto:gmx-users-request@**gromacs.org<[email protected]> >> >. >> 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> >> > >> >> >> >> >> -- >> Best, >> Liang Liu >> > > -- > ==============================**========== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > 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 [email protected] > 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 [email protected]. > Can't post? Read > http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> > -- Best, Liang Liu
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