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 <jalem...@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.
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Department of Biochemistry
Virginia Tech
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jalemkul[at]vt.edu | (540) 231-9080
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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
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