so everytime when the same trajectory file is read is it possible to randomize the velocity by a small amount so that i may end up with different trajectory?
sree. On Tue, Nov 30, 2010 at 7:28 AM, sreelakshmi ramesh < [email protected]> wrote: > Basically i have been using a sampling method called FFS to calculate the > rate constant for folding of a protein .The umbrella sampling done on the > system shows there is high barrier between the reac an prod states The phase > spece regions in ffs method are divided in to many non -intersecting > interfaces along the reaction coordinate.i have started the simulation from > reactant region and ended up at a point in between the reactant and product > state The transition state is not attained so far.The simulation is stopped > between the transition state and reactant .I have 100 such configuration > stored at that state.Now i have to select every config at that state at > random amd it should start with the same velocity when it was stored at > that state and continue the simulation to reach the next state.so i am > reading the position and velocities of the con-fig from previously saved > trajectory of that con-fig.so since randomly if the same con fig s selected > twice the trajectory is the same which i don't want. > Thats why i have been seeking the help of ll the people here.Thanks a lot > for ur patient reply. > > reagrds, > sree. > > On Tue, Nov 30, 2010 at 4:32 AM, Mark Abraham <[email protected]>wrote: > >> 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]>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]>> 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]>>> 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]>> >>>> >>>> >>>> >>>> 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 >>>> >>>> >>>> >>> -- >>> ======================================== >>> >>> 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 [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]. >>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>> >> >> >> >> -- >> >> gmx-users mailing list [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]. >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> > >
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