[gmx-users] changing the velocity in trajectory file

[sreelakshmi ramesh]

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 <jalemkul at 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 <jalemkul at vt.edu<mailto:
>> 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> <mailto: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 <http://vt.edu> | (540) 231-9080
>>
>>    http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>>    ========================================
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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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