[gmx-users] Initial velocity

Brighter Agyemang brighteragyemang at gmail.com
Mon May 13 08:23:29 CEST 2013

Thanks so much for your support,
The point is that, I have this mathematical theory on coarse grain
simulation for which is supposed to resolve the potential existing between
atoms suspended by an angle theta(like the triangle share for two atoms).
To solve for the potential, the theta between these two atoms has to be
resolved first and then with the use of some functions in the
math.h(acos,math.pow,log) I get the final potential. The mathematical model
has been resolved and I have coded everything in C. When I made inquiries
on how to implement it in GROMACS, I learnt that I have to modify the
bondfree.c file in ./src/gmxlib directory.
Theta is found based on the euclidian distance property and some
differentiation afterwards and this theta is then supplied together with
initial coordinates of the two atoms, boltzmann constant, and the mixing
paramter (fine grain + coarse grain) and then the potential is supposed to
be found.
My supervisor seems not to be remembering what he did some years ago with
GROMACS and it is really making life a though thing for me now
I hope this information will be useful, let me know if I still need to
clarify myself more pls.
The whole idea is the determine the potential existing between fine-grain
and coarse-grain multiscalled simulation

Thanks so much

On 13 May 2013 05:48, Acoot Brett <acootbrett at yahoo.com> wrote:

> Dear All,
> Will you please explain how the initial velocity may affect the MD
> results? What the initial velocity really means? How the velocity of the
> atoms in the protein changes in the MD process? What is the reasonable
> scope of the initial velocity? Any suggestions on how to manually input a
> defined initial velocity?
> Cheers,
> Acoot
> --
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