[Chimera-users] MD Simulation on Chimera

[Elaine Meng]

There is no such thing as "ideal system specification" because it always depends on your specific use case and the information you are trying to get.  It is beyond the scope of this mailing list to explain what all of the parameters mean and when they would be of most use. There are brief explanations of the Molecular Dynamics Simulation dialog settings in its help page, which you can see by clicking the Help button on the dialog, or see the copy at our website here:
<https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/md/md.html>

In general, this is a simple tool mainly used for teaching and small-molecule dynamics, or very limited structural relaxation of macromolecules.  Because the tool in Chimera is quite slow relative to other programs, it is not recommended for large (many-atom) systems, or long simulations, or for getting any quantitative result.  See these previous posts for more details and possibilities of other programs you could use instead.

<https://plato.cgl.ucsf.edu/pipermail/chimera-users/2020-September/017228.html>
<https://plato.cgl.ucsf.edu/pipermail/chimera-users/2020-September/017234.html>

I hope this clarifies the situation,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Oct 27, 2020, at 3:38 PM, Samiha I Amer <lanre.durojaye at yahoo.com> wrote:
> 
> Please may I know the ideal system specification to run a successful molecular Dynamics simulation on Chimera? Thank you