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 <jalem...@vt.edu
<mailto:jalem...@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 <qia...@gmail.com
<mailto:qia...@gmail.com> <mailto:qia...@gmail.com
<mailto:qia...@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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