[gmx-users] changing the velocity in trajectory file
sreelakshmi ramesh
sree.lakshmi at research.iiit.ac.in
Tue Nov 30 03:08:26 CET 2010
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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>>>>
>>> --
>>> ========================================
>>>
>>> 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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>>
>>
>>
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>>
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>
>
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