[email protected] wrote:
Sorry sree,
it still sounds like you want grompp with gen_vel=yes , as others have
suggested. You're going to need to explain it better if you want to get
more help. If you are saying that you need to *slightly* randomize the
velocities but not change them as much as by total reassignment, then
(a) I think that this is useless, just go with the reassignment
suggestion. (b) I may be missing something about your method, so if you
really want to randomize the velocities only slightly, then run a short
segment with the sd integrator (to do Langevin dynamics) and if you pass
that a different ld_seed every time (or better yet use ld_seed=-1) then
you will get exactly what you are asking for (although I still think
that velocity reassignment by grompp is faster and should be ok).
For what it's worth, long ago I did a test of gen_vel by manually setting values
that were very close together (literally gen_vel = 1, 2, 3) for three
"independent" simulations of an intrinsically disordered peptide. The
simulations converged to the same configurations (within a few decimal points
difference in the coordinates, but overall the secondary structure and overall
conformation were identical). Hence I would be very reluctant to think that
"slight" differences in velocities would generate very good sampling. Instead,
you may (perhaps erroneously) think that your simulations have beautifully
converged to the same result. Perhaps this is a limit of single precision, and
might be associated with Chris' point (a) above.
In contrast, by setting very different values of gen_vel (and the reason I do so
manually), I obtained results that agree better with experimental data in my
small test case, using what I might consider more truly "independent" simulation
conditions.
Maybe someone who knows more about the velocity randomization code can comment
further, but I think you're reached a consensus on what you should consider doing.
-Justin
Chris.
-- original message --
sreelakshmi ramesh sree.lakshmi at research.iiit.ac.in
Tue Nov 30 03:08:26 CET 2010
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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?
sree.
On Tue, Nov 30, 2010 at 7:28 AM, sreelakshmi ramesh <
sree.lakshmi at research.iiit.ac.in> wrote:
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.
Thats why i have been seeking the help of ll the people here.Thanks a lot
for ur patient reply.
reagrds,
sree.
On Tue, Nov 30, 2010 at 4:32 AM, Mark Abraham <Mark.Abraham at
anu.edu.au>wrote:
On 30/11/2010 2:16 AM, sreelakshmi ramesh wrote:
so can anybody tell me how to hack the trr file so that i can change the
velocity parameter in it
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.
Mark
On Mon, Nov 29, 2010 at 8:40 PM, Justin A. Lemkul <jalemkul at
vt.edu>wrote:
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 <jalemkul at
vt.edu<mailto:
jalemkul at 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 <qiaobf at
gmail.com
<mailto:qiaobf at gmail.com> <mailto: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 <http://vt.edu> | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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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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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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