[gmx-users] Initial velocity

Brighter Agyemang brighteragyemang at gmail.com
Mon May 13 15:45:30 CEST 2013


Please thanks so much for your support but I still do not get what all you
are talking about is....


On 13 May 2013 11:44, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 5/13/13 1:48 AM, Acoot Brett wrote:
>
>> Dear All,
>>
>> Will you please explain how the initial velocity may affect the MD
>> results?
>>
>
> We use different initial velocities to improve sampling, i.e. to allow the
> trajectory to evolve in different ways.  In the end, in the limit of
> infinite sampling, the trajectory ensemble averages should be the same.
>
>
>  What the initial velocity really means?
>>
>
> Just what it claims to be - the initial (first) velocities of each atom.
>
>
>  How the velocity of the atoms in the protein changes in the MD process?
>>
>
> Please read about MD integration algorithms.
>
>
>  What is the reasonable scope of the initial velocity?
>>
>
> I don't know what this means.
>
>
>  Any suggestions on how to manually input a defined initial velocity?
>>
>
> Provide grompp with an input file that has velocities - .trr, .edr, .gro,
> .cpt.
>
> -Justin
>
> --
> ==============================**==========
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
> ==============================**==========
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