[gmx-users] changing the velocity in trajectory file

sreelakshmi ramesh sree.lakshmi at research.iiit.ac.in
Tue Nov 30 02:58:05 CET 2010 

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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>>>
>>>
>> --
>> ========================================
>>
>> 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
>>
>> ========================================
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