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

Dear Elaine, thank you very much. I will study the links you sent me. I am almost new in the field of MD (I work mainly in the field of synthetic chemistry and spectroscopy), sorry for so many questions. What one can adfirm from the specific plot of RMSD vs trajectory frame number I sent you in my previous email (attached)? Was the system stabilized enough to adfirm that the structure present at the end of the simulation is 'realistic'? Another question, you already explained me that for long simulations and for quantitative scopes Chimera MD is not the ideal. Does it mean that it will not work or that it could work but with not realistic results? I wonder if your team will consider to improve in the future the MD tool extending it to larger molecular systems and also rendering suitable for longer simulation times. In fact, I find Chimera easier and more user-friendly than other programs. Thank you and 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@unina.it giovanni.roviello@cnr.it http://www.ibb.cnr.it/?command=viewu&id=387&lang=en https://orcid.org/0000-0001-6065-2367 Elaine Meng ha scritto:

Dear Giovanni, The X-axis of the plot shows the trajectory frame number, i.e. 10 means the 10th set of coordinates in whatever trajectory you are viewing.

From the MD Movie help: "Clicking Plot plots the measurement value versus trajectory frame number."

https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movie/framemovie.... https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movie/movie.html#...

How many time steps per trajectory frame depends on what value you chose in the Molecular Dynamics tool, Run Parameters, Other Runtime Options section, "Save once every [N] steps" (default N=10). I don't know if you saved equilibration and production all in one trajectory file or in two separate trajectory files, and if the latter, I don't know which trajectory you are viewing in the MD Movie tool. However, if the save option N= 10 and your time step is 1 fs, then each 1 on the x axis of the plot = 10 fs of time.

https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/md/md.html https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/md/md.html#run

There is no way in Chimera to combine different kinds of measurements into a single plot, sorry. You would need to use the "Dump Values" button at the bottom of each plot to save the values to a text file, and then use all these text files of values in some other plotting software. This Dump Values button is mentioned at the end of the MD Movie help section on plotting. https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movie/movie.html#...

I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

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On Jan 29, 2021, at 3:30 AM, Giovanni Roviello wrote:

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@unina.it giovanni.roviello@cnr.it

http://www.ibb.cnr.it/?command=viewu&id=387&lang=en https://orcid.org/0000-0001-6065-2367

Elaine Meng 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.htm... https://plato.cgl.ucsf.edu/pipermail/chimera-users/2020-September/017234.htm...

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

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On Jan 24, 2021, at 6:37 AM, Giovanni Roviello 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@unina.it giovanni.roviello@cnr.it

http://www.ibb.cnr.it/?command=viewu&id=387&lang=en https://orcid.org/0000-0001-6065-2367

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