[Chimera-users] simulation of 40 ns using the Chimera program

[Elaine Meng]

Dear Dr. Sefa Celik ,
The total time is number of simulation steps multiplied by time per step.  N is not part of this calculation. N is just how often to save output coordinates, and the bigger the N, the farther apart in time each saved frame will be.  You could do a really long simulation and only save 2 frames to look at, for example.

In general, however, Chimera is not recommended for very long MD simulations.  You should instead use a program that is primarily for simulations, such as AMBER or GROMACS, as they will be much more time-efficient and give more parameter options.
Best,
Elaine
-----
Elaine C. Meng, Ph.D.
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Jan 31, 2019, at 4:24 AM, SEFA ÇELİK <scelik at istanbul.edu.tr> wrote:
> 
> Dear Dr.
> I want to do a simulation of 40 ns using the Chimera program. What values should I use for this? For example, when I choose 200000 steps for equilibrate and 200000 steps for production phase, the result is 40000 frames. That is, N = 10 and 40000 * 10 = 400000 fs ie 400 ps = 0.4 ns . But I want to do the calculation for 40 ns.
> I'm looking at other runtime options, N = 10.
> Can you give some values for a simulation of 40 ns?
> 
> Can you help with this? Could you explain in detail?
> Best regard
> Assoc Prof. Dr. Sefa Celik  
> 
> 
> 
> Elaine Meng <meng at cgl.ucsf.edu>, 1 Eki 2018 Pzt, 22:17 tarihinde şunu yazdı:
> Dear Dr. Sefa Celik,
> The “frames” are already “time” — each time step saved is one frame in MD Movie. I do not know if you are viewing the equilibration trajectory output or the production trajectory output, but both of those dialogs say “Time step (fs) = 1” and  5000 steps.  However, you have 1001 and not 5000.  You did not show the other “Other runtime options” section which includes “Save once every [N] steps” where N is some integer. 
> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/md/md.html#other>
> 
>  How to convert between time and frames is 1 frame = N (1 fs), but you would have to look in the "Other runtime options" to see what you used for N. Maybe it’s 5. The extra 1 frame is probably just the starting structure.
> 
> If you mean you want the graph to say “time” instead of “frames,” sorry there is no option to do that.  You’d have to use the “Dump Values” button at the bottom of the graph dialog to save the values to a text file and then use some other program to make a graph with the labels etc. that you want.  
> 
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> 
> > On Sep 30, 2018, at 11:28 PM, SEFA ÇELİK <scelik at istanbul.edu.tr> wrote:
> > 
> > Dear Dr.
> > 
> > I am using Chimera software(windows platform). I tried to get rmsd graph(using the plotting in the MD Movie trajectory viewer). And I got the result. But, graph's x-axis "frame" and y-axis "rmsd" value. I want the x axis to be the "time".  Briefly, I want to see how the value of rmsd changes with time.
> > I added files to the e-mail. Can you explain what "1001 frames" mean? And how do I convert "1001 frames" to time. I want to see the RMSD change by time.
> > Can you help with this? Could you explain in detail?
> > 
> > Best regard
> > 
> > Assoc Prof. Dr. Sefa Celik
> > <chimera-5.jpg><chimera-4.jpg><chimera-1.jpg><chimera-3.jpg><chimera-2.jpg>
> 
> 
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