[Chimera-users] MD simulation in Chimera : 10 ns simulation is equivalent to 1 million of production steps 10 fs each?
Giovanni Roviello
giroviel at unina.it
Fri Jan 29 10:00:36 PST 2021
Dear Elaine,
thank you for your email. I will take in consideration all your
explainations and suggestions. What is sure I will have to study a lot
to obtain some rationale results by MD.
Thank you again 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 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,
> Sorry, it is beyond the scope of this software e-mail help address
> to give general research advice or teach about molecular modeling.
> I can only recommend reading papers with similar studies, or
> textbooks on molecular modeling, or talking to any colleagues with
> more experience in modeling and molecular dynamics.
>
> The MD tool in Chimera is slow to calculate, does not provide access
> to very many simulation parameters, or allow much control over
> parametrization of nonstandard residues like ligands, or include as
> much information in the output as dedicated dynamics packages
> (Amber, Gromacs, etc.). Thus you will not be able to get quantities
> such as free energy differences (because they are not in the
> output), and it will not be possible (or very difficult) to run the
> longer calculations required for precision anyway because it will
> take too long, and you may not be able to use settings that might be
> needed for accurate results in your specific situation, because the
> software does not have controls for those settings.
>
> The MD simulation tool was developed in collaboration with another
> group, who did much of the work. Chimera is no longer funded for any
> active development, we are only maintaining it currently.
>
> Again, in my first reply mail I gave links that included advice on
> other software you could use (Amber etc.). Yes they will be harder
> to learn and use, but that is because molecular dynamics simulations
> are complicated. In order to do a good simulation, you will need to
> understand many different parameters in order to set them correctly
> for your specific project.
>
> I hope this helps,
> Elaine
>
>
>> On Jan 29, 2021, at 9:18 AM, Giovanni Roviello <giroviel at unina.it> wrote:
>>
>> 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 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,
>>> 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.html>
>>> <https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movie/movie.html#plotting>
>>>
>>> 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#plotting>
>>>
>>> I hope this helps,
>>> Elaine
>>> -----
>>> Elaine C. Meng, Ph.D.
>>> UCSF Chimera(X) team
>>> Department of Pharmaceutical Chemistry
>>> University of California, San Francisco
>>>
>>>> On Jan 29, 2021, at 3:30 AM, Giovanni Roviello <giroviel at unina.it> 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 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
>>>>>>
>>>>>
>>>>>
>>>>
>>>> <goodMDRMSD.png>_______________________________________________
>>>> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
>>>> Manage subscription:
>>>> https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
>>>
>>>
>>
>> <goodMDRMSD.png>
>
>
More information about the Chimera-users
mailing list