so can anybody tell me how to hack the trr file so that i can change the velocity parameter in it
On Mon, Nov 29, 2010 at 8:40 PM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > sreelakshmi ramesh wrote: > >> so if i use gen_vel = yes ad seed -1 i get diff traj.But what would happen >> if read the postion and velocity from traj file(input file) >> >> > When you supply a .trr file in conjunction with "gen_vel = yes," the > position is taken but the velocities are ignored. grompp tells you this > fact, as well. > > -Justin > > On Mon, Nov 29, 2010 at 8:08 PM, Justin A. Lemkul <jalem...@vt.edu<mailto: >> jalem...@vt.edu>> wrote: >> >> >> >> sreelakshmi ramesh wrote: >> >> i am reading the velocities from trajectory file.so i dont want >> the maxwellain distribution of veloc thats y i have set gen_vel=no. >> >> >> >> Generating velocities is the only way to get new ones to start >> independent trajectories. Otherwise, you'd have to somehow manually >> hack your .trr file to write new velocities manually. If your >> objective is to start 20 independent trajectories, then "gen_vel = >> yes" in conjunction with not using your .trr file sounds like the >> way to go. >> >> -Justin >> >> sree >> >> >> On Mon, Nov 29, 2010 at 7:32 PM, Baofu Qiao <qia...@gmail.com >> <mailto:qia...@gmail.com> <mailto:qia...@gmail.com >> >> <mailto:qia...@gmail.com>>> wrote: >> >> >> Why don't use different random (gen_vel =yes; gen_seed =-1 in >> .mdp >> file) seed to generate the velocity? >> >> >> On 11/29/2010 02:55 PM, sreelakshmi ramesh wrote: >> > Dear all, >> > could anybody help me out with the following >> issue. >> I have a >> > trajectory file.i have to used that file at a particular >> frame >> as the >> > input to continue the simulation and i need to use that >> file for 20 >> > independent simulations.since the starting file for the 20 >> simulations are >> > the same coordinate and velocity the 20 simulations are >> producing the same >> > output trajectory.so is there a way to change the velocity >> by a >> small >> > value in the input trajectory file so that every time i >> can get a >> diff >> > trajectory from same input file. >> > >> > reagrds, >> > sree. >> > >> > >> >> -- >> gmx-users mailing list gmx-users@gromacs.org >> <mailto:gmx-users@gromacs.org> >> <mailto: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> >> <mailto:gmx-users-requ...@gromacs.org >> <mailto:gmx-users-requ...@gromacs.org>>. >> >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> >> >> -- ======================================== >> >> 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 >> >> 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 >> >> >> > -- > ======================================== > > 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 >
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