[gmx-users] changing the velocity in trajectory file

[Justin A. Lemkul]

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

========================================