bharat gupta wrote:
Sorry to ask this question but setting the gen_vel=yes and gen_seed = -1
will eventually lead to different simulation and thus different
simulated structures ?? .. and after completing one set of simulation
with this paramter and 3ns time .. do i have to repeat it some 3 or more
times ??.... pls comment.. as I am going to start simulation with these
parameters.
As I have already said, the combination of velocity generation with a different
random seed will give you (in theory) independent trajectories. How many
replicates you run is up to you. I certainly hope that, after all I've said,
you're still not intending on simply running 3-ns simulations, regardless of how
many replicates you run. If you're looking at loop movements, you won't answer
your questions with such little data.
-Justin
On Wed, Feb 2, 2011 at 5:27 AM, Justin A. Lemkul <jalem...@vt.edu
<mailto:jalem...@vt.edu>> wrote:
bharat gupta wrote:
Thanks for such a detailed reply to my queries .. But conducting
a 50ns simulation will take time ... so i want to conduct
independent simulation and for that I searched some threads but
was not able to get the proper description and method... if u
can guide me through an appropriate link .. it would be much
more helpful ..
Each simulation begins with the assignment of random velocities
(gen_vel = yes). Specify different values of gen_seed (or leave it
set to -1) to get different velocities each time.
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
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jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
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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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