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).
Chris.
-- original message --
sreelakshmi ramesh sree.lakshmi at research.iiit.ac.in
Tue Nov 30 03:08:26 CET 2010
* Previous message: [gmx-users] changing the velocity in trajectory file
* Next message: [gmx-users] Re: error in grompp command
* Messages sorted by: [ date ] [ thread ] [ subject ] [ author ]
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.
>
>
--
gmx-users mailing list gmx-users at gromacs.org
<mailto:gmx-users at gromacs.org>
<mailto:gmx-users at gromacs.org <mailto:gmx-users at
gromacs.org>>
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before
posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-request at gromacs.org
<mailto:gmx-users-request at gromacs.org>
<mailto:gmx-users-request at gromacs.org
<mailto:gmx-users-request at gromacs.org>>.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
-- ========================================
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
========================================
-- gmx-users mailing list gmx-users at gromacs.org
<mailto:gmx-users at gromacs.org>
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the www
interface or send it to gmx-users-request at gromacs.org
<mailto:gmx-users-request at gromacs.org>.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
--
========================================
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
========================================
--
gmx-users mailing list gmx-users at gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the www
interface or send it to gmx-users-request at gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
--
gmx-users mailing list gmx-users at gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-request at gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
--
gmx-users mailing list [email protected]
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [email protected].
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
