[gmx-users] changing the velocity in trajectory file
Mark Abraham
Mark.Abraham at anu.edu.au
Tue Nov 30 00:02:31 CET 2010
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
> <mailto: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>
> <mailto: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>>
> <mailto: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> <http://vt.edu> | (540)
> 231-9080
>
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
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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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