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

SEFA ÇELİK scelik at istanbul.edu.tr
Thu Jan 31 04:24:15 PST 2019

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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