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)<br><br><div class="gmail_quote">On Mon, Nov 29, 2010 at 8:08 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;"><div class="im"><br>
<br>
sreelakshmi ramesh wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
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.<br>
<br>
<br>
</blockquote>
<br></div>
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.<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
sree<div class="im"><br>
<br>
On Mon, Nov 29, 2010 at 7:32 PM, Baofu Qiao <<a href="mailto:qiaobf@gmail.com" target="_blank">qiaobf@gmail.com</a> <mailto:<a href="mailto:qiaobf@gmail.com" target="_blank">qiaobf@gmail.com</a>>> wrote:<br>
<br>
<br>
Why don't use different random (gen_vel =yes; gen_seed =-1 in .mdp<br>
file) seed to generate the velocity?<br>
<br>
<br>
On 11/29/2010 02:55 PM, sreelakshmi ramesh wrote:<br>
> Dear all,<br>
> could anybody help me out with the following issue.<br>
I have a<br>
> trajectory file.i have to used that file at a particular frame<br>
as the<br>
> input to continue the simulation and i need to use that file for 20<br>
> independent simulations.since the starting file for the 20<br>
simulations are<br>
> the same coordinate and velocity the 20 simulations are<br>
producing the same<br>
> output trajectory.so is there a way to change the velocity by a<br>
small<br>
> value in the input trajectory file so that every time i can get a<br>
diff<br>
> trajectory from same input file.<br>
><br>
> reagrds,<br>
> sree.<br>
><br>
><br>
<br>
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-- <br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
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