Hi This is regarding the pull code.. I have followed your tutorial to get the PMF for distance between 2 atoms using the pull code. I want to know if one can bring the atoms closer rather than pull them apart? I want to start from the maximum distance and then bring them closer to check reversibility. Also, I dont think I can apply it a fixed vector (as in specify the vector from one atom to the other) because I dont think the path will be a straight line.
Pooja On Fri, Apr 1, 2011 at 8:02 PM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > Sai Pooja wrote: > >> The pull tutorial uses npt simulations.. is that required by the algorithm >> or can one use nvt after the system has been sufficiently equilibrated using >> npt? >> >> > Use whatever conditions are appropriate for your system. Tutorials should > not be viewed as the only applicable conditions, merely one such example of > what might be done. > > -Justin > > On Fri, Apr 1, 2011 at 7:32 PM, Justin A. Lemkul <jalem...@vt.edu<mailto: >> jalem...@vt.edu>> wrote: >> >> >> pdb2gmx -chainsep (-merge in 4.0.x and before) should allow you to >> create a merged [moleculetype] to apply distance restraints. If >> you're just trying to use a harmonic potential to define some >> sampling distance (for US), then distance restraints are not >> necessary, just apply the pull code. >> >> -Justin >> >> Sai Pooja wrote: >> >> Also, the chains do not diffuse apart in time since they are >> position restrained(some parts of each chain are ...) >> >> On Fri, Apr 1, 2011 at 7:26 PM, Sai Pooja <saipo...@gmail.com >> <mailto:saipo...@gmail.com> <mailto:saipo...@gmail.com >> >> <mailto:saipo...@gmail.com>>> wrote: >> >> Hi, >> I have 5 chains in my Protein. I want to apply distance >> restraints >> for doing Umbrella Sampling for 2 atoms on different chains. Is >> there a way to do this since the two chains have separater >> itp files. >> Pooja >> >> -- Quaerendo Invenietis-Seek and you shall discover. >> >> >> >> >> -- Quaerendo Invenietis-Seek and you shall discover. >> >> >> -- ======================================== >> >> 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 >> >> ======================================== >> -- gmx-users mailing list gmx-users@gromacs.org >> <mailto: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 >> <mailto:gmx-users-requ...@gromacs.org>. >> >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> >> >> >> -- >> Quaerendo Invenietis-Seek and you shall discover. >> > > -- > ======================================== > > 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 > > ======================================== > -- > 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 > -- Quaerendo Invenietis-Seek and you shall discover.
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