- Видео 24
- Просмотров 195 227
SimbiosOpenMM
Добавлен 16 фев 2013
OpenMM is a toolkit for molecular simulation. It can be used either as a stand-alone application for running simulations, or as a library you call from your own code. It provides a combination of extreme flexibility (through custom forces and integrators), openness, and high performance (especially on recent GPUs) that make it truly unique among simulation codes.
OpenMM is developed at Simbios, a National Center for Biomedical Computing that researches and develops software for physics-based simulations of biological structures. Funded by the National Institutes of Health, Simbios is based at Stanford University and has a network of collaborators throughout the world.
OpenMM is developed at Simbios, a National Center for Biomedical Computing that researches and develops software for physics-based simulations of biological structures. Funded by the National Institutes of Health, Simbios is based at Stanford University and has a network of collaborators throughout the world.
Видео
Exercise: Performing Analysis with MDTraj
Просмотров 5 тыс.10 лет назад
Exercise: Performing Analysis with MDTraj
Introduction to Molecular Dynamics Trajectory Analysis and Markov State Models (MSM)
Просмотров 13 тыс.10 лет назад
Introduction to Molecular Dynamics Trajectory Analysis and Markov State Models (MSM)
Exercise: Heating and Constraining Particles to Simulate a Protein-Ligand System
Просмотров 1 тыс.10 лет назад
Exercise: Heating and Constraining Particles to Simulate a Protein-Ligand System
Introduction to Running Simulations with OpenMM
Просмотров 1,6 тыс.10 лет назад
Introduction to Running Simulations with OpenMM
Introduction to Molecular Dynamics Workflows and Tools
Просмотров 5 тыс.10 лет назад
Introduction to Molecular Dynamics Workflows and Tools
Extracting Energies and Other Quantities from Simulations
Просмотров 23511 лет назад
Extracting Energies and Other Quantities from Simulations
Creating and Customizing Force Fields in OpenMM
Просмотров 2,8 тыс.11 лет назад
Creating and Customizing Force Fields in OpenMM
Customizing Forces and Integrators with OpenMM
Просмотров 68811 лет назад
Simbios Senior Software Developer Peter Eastman discusses customizing forces and integrators with OpenMM at the OpenMM Workshop held at Stanford University on March 26-29, 2013.
Exercise: The Basics of OpenMM Molecular Dynamics Simulations
Просмотров 1,9 тыс.11 лет назад
Simbios Postdoctoral Fellow Gert Kiss leads an interactive exercise which explores the basics of OpenMM simulations. The presentation was given at the OpenMM Workshop held at Stanford University on March 26-29, 2013.
Introduction to the OpenMM API
Просмотров 91911 лет назад
Simbios Senior Software Developer Peter Eastman presents an introduction to the OpenMM API.
Introduction to Running Simulations with OpenMM
Просмотров 2,8 тыс.11 лет назад
Simbios Senior Software Developer Peter Eastman introduces running simulations with OpenMM at the OpenMM workshop held at Stanford University on March 26-29, 2013.
Exercises: Running Simulations with OpenMM
Просмотров 7 тыс.11 лет назад
Exercises: Running Simulations with OpenMM
Customizing Forces and Integrators with OpenMM
Просмотров 89311 лет назад
Customizing Forces and Integrators with OpenMM
Using AMOEBA Polarizable Force Fields
Просмотров 2,5 тыс.11 лет назад
Using AMOEBA Polarizable Force Fields
Introduction to Markov State Models for Trajectory Analysis
Просмотров 10 тыс.11 лет назад
Introduction to Markov State Models for Trajectory Analysis
Introduction to Running Simulations with OpenMM
Просмотров 9 тыс.11 лет назад
Introduction to Running Simulations with OpenMM
Insane content
Which integrator do you use for thermaldynamic integration? Do you use openmmtools.integrators.NonequilibriumLangevinIntegrator?
Man, I miss working with GROMACS. The humour aspect made it just that more interesting XD
it's a good lecture but the mic peaking really distracts and annoys the hell out of me. (i have misophonia)
Are we in the future yet
Who is the person teaching here? You should have mentioned his identity to give him credit for this nice lecture.
i believe his name is in first slide
Great presentation. It looks like I am not going to escape not being able to code as a chemist💀
Great lecture for beginners! Thank you!
Interesting
Just a comment about audio.. It is only one channel and sounds only comes in one speaker. This can cause issues sometimes
Hello, can we use MDtraj for .xyz files?
Mad nice, homie.
Very nice presentation. Thanks.
Very informative presentation! Thank you!
When listening with headphones the audio is only in one headphone, just FYI! Great presentation Lee-Ping :)
Natalya G I noticed this as well. You can set your smart phone to output all audio as mono and it wi them push this one channel stereo out both ear phones.
MDTraj is a amazing package. thx
Are the exercice material accessible ?
Thank you
This is very nice but it would be nicer if you could fix the audio.
Very interesting but hardly about OpenMM.
A very inspiring presentation on MD. Good job!
You are an awesome speaker!
I like this lecture very much. The lecture gave a good balance between theoretical details and practical needs. Difficult concepts are explained in a language that anybody with a science degree can understand.
Great video, i suggest using CC because the audio is full of clipping and buzzing (also only on the left side)
Hi professor. I'm currently and undergrad Biochemistry student. What is the computational requirement to simulate a cell or even an organ down to the atomic level? How long will it take to render a few seconds animation on a modern super computer? And on a quantum computer? Thank you.
Hi, i have the same question, i was wondering if you've found an answer and could share it here.
A cell would be way too complex to be simulated. At least without 9000 potential confounding factors and lacking physiological signals. An organ? Lmao
Hi professor. What is the computational requirement to simulate a cell or even an organ down to the atomic level? How long will it take to render a few seconds animation on a modern super computer? And on a quantum computer?
Quantum computing is not a practical technology just yet, and using the highest performances computers of today, putting 20,000 particles (mostly water) in a box to simulate could take days to reach ~200ns. So yeah, no cells and no organs anytime soon, but extremely practical applications in drug discovery.
I liked it :-), thank to the lecturer
It is now April 2018. Why is this the latest video, yet it is 4 years old? Not a good state of technology, when this video is titled "The Future of Molecular Dynamics".
great
Nice job! Concise but very helpful, Thank you!
It is very nice workflow (I mean using python interface) but I have hard time figure out how to use it for anything else than proteins in water (I want to use it for bunch of small molecules ... ). In particular I don't know how to make .pdb file in such a way that functions like PDBFile() and forcefield.createSystem() are able to derive topology from it. If I created the .pdb file using e.g. Avogadro, I get lot of errors saying that it does not understand my .pdb file :((((.
It sounds like you need parameters for your small molecule. Sorry if you are aware of this already, but anytime you try to simulate something other than the traditional 20 amino acids, and maybe water and ions, you need to provide a set of parameters so the simulation knows how to treat your special molecules. If its a common compound it may be available online, otherwise you need to use something like CHARMM or Antechamber. I recommend Antechamber, because I've found it to be a bit more user friendly. Its part of the Amber package which many institutes have a license for. I realize this is 5 years late, but maybe someone else will find it useful.
wow! How were you able to do the time evolution graphs with the MD trajectory on the phase diagram slide? Great presentation btw.
I only noticed these comments today, thank you for the compliment! I drew the order parameter histograms in Matplotlib and composed the images with VMD screenshots, then compressed them into a movie. (At least I think that's what I did; it was a long time ago).
nice introduction but sound is horrible.. sad story :( scratching FX
Great presentation. Thanks for posting on the internet.
what do you mean by sharing thermodynamic weights at @8.04. Why can't I have just 2 lambdas ? Could you explain that part.
Where I can get rest of the lectures in this series?
am i supposed to understand this at derivation level?
You can learn more about the derivations through an introductory text on quantum chemistry.
very useful
thanks for informations......sir
nice.....
Very useful. Thx for a quick course online.
what a douche
Please can I have this PPT with references ? please :email nilesh@icgeb.res.in
Awesome lecture
Very helpful. Thank you!
Mute...? ((
Could you make a video on how to arrest a specific frame of a trajectory please?
you first have to tell it that it has the right to remain silent that anything it says can and will be used against it in the court of law
Was the tutorial recorded? Would be interested in checking that out!
My left ear enjoined this, my right was just calmed by the gentle white noise.
Lovely intro