[Chimera-users] MD simulation in Chimera : 10 ns simulation is equivalent to 1 million of production steps 10 fs each?
giroviel at unina.it
Sun Jan 24 09:34:54 PST 2021
thank you very much for your fast answer and for your useful information.
Dr. Giovanni N. Roviello, Ph.D.
Researcher at Istituto di Biostrutture e Bioimmagini
IBB - CNR; Via Mezzocannone 16; I-80134
giroviel at unina.it
giovanni.roviello at cnr.it
Elaine Meng <meng at cgl.ucsf.edu> ha scritto:
> 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.
> I hope this clarifies the situation,
> 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
>> Thank you in advance for your kind help.
>> Kind regards,
>> 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
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