On 30/11/2010 2:16 AM, sreelakshmi ramesh wrote:
so can anybody tell me how to hack the trr file so that i can change the velocity parameter in it
You've expressed no reason to need to do that rather than generate independent random sets of velocities. If you're going to ignore the advice you've been given, you'll have to justify that decision in order that people might think you're not just going to ignore further advice, too :-) Our time is valuable, and we might choose to spend it on people who look like they value it.
Mark
On Mon, Nov 29, 2010 at 8:40 PM, Justin A. Lemkul <[email protected] <mailto:[email protected]>> 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 <[email protected] <mailto:[email protected]> <mailto:[email protected] <mailto:[email protected]>>> 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 <[email protected] <mailto:[email protected]> <mailto:[email protected] <mailto:[email protected]>> <mailto:[email protected] <mailto:[email protected]> <mailto:[email protected] <mailto:[email protected]>>>> 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 [email protected] <mailto:[email protected]> <mailto:[email protected] <mailto:[email protected]>> <mailto:[email protected] <mailto:[email protected]> <mailto:[email protected] <mailto:[email protected]>>> 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 [email protected] <mailto:[email protected]> <mailto:[email protected] <mailto:[email protected]>> <mailto:[email protected] <mailto:[email protected]> <mailto:[email protected] <mailto:[email protected]>>>. 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> <http://vt.edu> | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ======================================== -- gmx-users mailing list [email protected] <mailto:[email protected]> <mailto:[email protected] <mailto:[email protected]>> 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 [email protected] <mailto:[email protected]> <mailto:[email protected] <mailto:[email protected]>>. 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 [email protected]<mailto:[email protected]> 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 [email protected] <mailto:[email protected]>. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
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