From: Leandro Martinez (lmartinez_at_iqm.unicamp.br)
Date: Thu Jun 03 2004 - 11:47:05 CDT
I guess you are talking about steered molecular dynamics. I think
you should actually check how long you want your simulation to
be and test a few velocities in such a way that the event you
are expecting occurs in that simulation time. Lower velocities provide
a better sampling of the phase space and hence your simulation
is more representative of the dynamics of the real system. However,
of course, you are trying to induce something to happen, and so you
should do it in such a way that it occurs in a reasonable simulation
time. At least for ligand dissociation, for example, you should
choose the velocity in that way. Of course, you can get good
guesses from Schulten's papers.
On Thursday 03 June 2004 12:17, Uday Chippada wrote:
> I was doing the constant velocity simulation for 1A3J obtained from
> Protein Data Bank. How would I know exactly what velocity I should be
> pulling the atom. Is there any specific velocity? Or do we have to
> calculate it? If we have to calculate, how do we do it?
> Any help is appreciated.
> Uday Chippada
> Graduate Student
> Dept. of Mechanical and Aerospace Engineering
> Rutgers University, New Jersey
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