[gmx-users] changing the velocity in trajectory file

[sreelakshmi ramesh]

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)

On Mon, Nov 29, 2010 at 8:08 PM, Justin A. Lemkul <jalemkul at 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 <qiaobf at gmail.com <mailto:
>> qiaobf at 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.
>>     >
>>     >
>>
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> --
> ========================================
>
> 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
>
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