[gmx-users] changing the velocity in trajectory file

[Justin A. Lemkul]

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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