[Chimera-users] MD simulation in Chimera : 10 ns simulation is equivalent to 1 million of production steps 10 fs each?

[Elaine Meng]

Dear Giovanni,
Time step multiplied by number of steps is the total time.  However, we do not provide detailed advice over what settings you should use, because it always depends on your specific project. 

However, Chimera is not recommended for long simulations or calculating precise quantities: In general, the Molecular Dynamics Simulation tool 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 Jan 24, 2021, at 6:37 AM, Giovanni Roviello <giroviel at unina.it> wrote:
> 
> Dear Sirs,
> 
> I would like to perform a MD simulation by UCSF Chimera.
> 
> Should I wish to perform a 10 ns simulation (for example) how could I set the parameters related to time? For example in production a number of phase steps of 1000000 and a time step of 10 fs is OK?
> 
> Does the relaxation time Nosé thermostat has effect on the overall simulation time?
> 
> In simpler words if I set 1000000 steps, 10 fs time step, and I leave selected Nosè thermostat with 0.2 ps (but leave unselected the barostat option) will it correspond to a 10 ns MD simulation?
> 
> Of course if I will publish using Chimera I will cite the program and the reference as indicated in
> 
> https://www.cgl.ucsf.edu/chimera/docs/credits.html
> 
> Thank you in advance for your kind help.
> 
> Kind regards,
> 
> Giovanni
> _______________________________________________________
> Dr. Giovanni N. Roviello, Ph.D.
> Researcher at Istituto di Biostrutture e Bioimmagini
> IBB - CNR; Via Mezzocannone 16; I-80134
> Naples; Italy
> giroviel at unina.it
> giovanni.roviello at cnr.it
> 
> http://www.ibb.cnr.it/?command=viewu&id=387&lang=en
> https://orcid.org/0000-0001-6065-2367
> 
> 
> 
> 
> 
> 
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