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

[Giovanni Roviello]

Dear Elaine,

thank you very much for your fast answer and for your useful information.

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



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.
>
> <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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>
>