[gmx-users] Initial velocity

[Justin Lemkul]

On 5/13/13 9:45 AM, Brighter Agyemang wrote:
> Please thanks so much for your support but I still do not get what all you
> are talking about is....
>

These posts are not related to your question.  Reading posts on other topics can 
be very informative and should be augmented by literature and textbook reading.

-Justin

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

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

========================================