so everytime when the same trajectory file is read is it possible to randomize the velocity by a small amount so that i may end up with different trajectory?<br><br>sree.<br><br><div class="gmail_quote">On Tue, Nov 30, 2010 at 7:28 AM, sreelakshmi ramesh <span dir="ltr"><<a href="mailto:sree.lakshmi@research.iiit.ac.in" target="_blank">sree.lakshmi@research.iiit.ac.in</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;">Basically i have been using a sampling method called FFS to calculate the rate constant for folding of a protein .The umbrella sampling done on the system shows there is high barrier between the reac an prod states The phase spece regions in ffs method are divided in to many non -intersecting interfaces along the reaction coordinate.i have started the simulation from reactant region and ended up at a point in between the reactant and product state The transition state is not attained so far.The simulation is stopped between the transition state and reactant .I have 100 such configuration stored at that state.Now i have to select every config at that state at random amd it should start with the same velocity when it was stored at that state and continue the simulation to reach the next state.so i am reading the position and velocities of the con-fig from previously saved trajectory of that con-fig.so since randomly if the same con fig s selected twice the trajectory is the same which i don't want.<br>
Thats why i have been seeking the help of ll the people here.Thanks a lot for ur patient reply.<br><br>reagrds,<br>sree.<br><br><div class="gmail_quote"><div><div></div><div>On Tue, Nov 30, 2010 at 4:32 AM, Mark Abraham <span dir="ltr"><<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a>></span> wrote:<br>
</div></div><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;"><div><div></div><div>
<div text="#000000" bgcolor="#ffffff"><div>
On 30/11/2010 2:16 AM, sreelakshmi ramesh wrote:
<blockquote type="cite">so can anybody tell me how to hack the trr file so
that i can change the velocity parameter in it<br>
</blockquote>
<br></div>
You've expressed no reason to need to do that rather than generate
independent random sets of velocities. If you're going to ignore the
advice you've been given, you'll have to justify that decision in
order that people might think you're not just going to ignore
further advice, too :-) Our time is valuable, and we might choose to
spend it on people who look like they value it.<br><font color="#888888">
<br>
Mark</font><div><div></div><div><br>
<br>
<blockquote type="cite"><br>
<div class="gmail_quote">On Mon, Nov 29, 2010 at 8:40 PM, Justin
A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu" target="_blank">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><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;">
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>
</blockquote>
<br>
</div>
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.<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;">
<div>
On Mon, Nov 29, 2010 at 8:08 PM, Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>>> wrote:<br>
<br>
<br>
<br>
sreelakshmi ramesh wrote:<br>
<br>
i am reading the velocities from trajectory file.so
i dont want<br>
the maxwellain distribution of veloc thats y i have
set gen_vel=no.<br>
<br>
<br>
<br>
Generating velocities is the only way to get new ones
to start<br>
independent trajectories. Otherwise, you'd have to
somehow manually<br>
hack your .trr file to write new velocities manually.
If your<br>
objective is to start 20 independent trajectories, then
"gen_vel =<br>
yes" in conjunction with not using your .trr file
sounds like the<br>
way to go.<br>
<br>
-Justin<br>
<br>
sree<br>
<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><br>
</div>
<mailto:<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>
<div>
<div><br>
<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<br>
.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<br>
issue.<br>
I have a<br>
> trajectory file.i have to used that file
at a particular<br>
frame<br>
as the<br>
> input to continue the simulation and i
need to use that<br>
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<br>
by a<br>
small<br>
> value in the input trajectory file so
that every time i<br>
can get a<br>
diff<br>
> trajectory from same input file.<br>
><br>
> reagrds,<br>
> sree.<br>
><br>
><br>
<br>
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