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

[Giovanni Roviello]

Dear Elaine,

I performed a MD simulation with 500000 (5.10^5) equilibration stes  
(time step 1 fs) and 5000 production steps (time step 1 fs). I  
obtained the attached RMSD Plot. I see RMSD values (Angstrom?) plotted  
against an unspecified 'x' ranging from 0 to 50000 (5.10^4). What do I  
have: time as ps?

I also wonder how I can save the MD movie window (with Analysis  
function) that appears after MD completion in view of reopening PLOTS  
in future and how can open the saved PLOTS (as .eps, .ps, .raw, .svg  
files), overlay each other,  in other words which software I can use  
to elaborate, overlay etc the Plots obtained by CHIMERA after  
different MD runs.

Thank you a lot for your assistance.

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
>>
>>
>>
>>
>>
>>
>> _______________________________________________
>> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
>> Manage subscription:  
>> https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
>>
>
>

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