[gmx-users] changing the velocity in trajectory file

Justin A. Lemkul jalemkul at vt.edu
Tue Nov 30 04:19:42 CET 2010



chris.neale at utoronto.ca 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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>>>>>
>>>>>
>>>> -- 
>>>> ========================================
>>>>
>>>> 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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> 
> 

-- 
========================================

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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