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maccallumlab / martini_openmm

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Tutorial example script? #1

Open phisanti opened 3 years ago

phisanti commented 3 years ago

Hello!

I am a bit new to MD, so I might be asking for something extraordinarily simple or impossible. So far I have been doing all-atom simulations with openMM in a membrane protein. They look all great, but it seems that the real interesting part happens at longer time scales.

Therefore, I am considering using trying dry Martini! I read everywhere that for long time scales, or very complex systems, coarse-grained simulations simplify the model. That saving in computing effort allows doing longer MD time. I have looked around the repository and on the web, but I could not find any "recipe-type " script. Thus, I was wondering if it would be possible to include a simple python script that would do something like:

from martini_openmm import *

prot = load_prot_and_top()

martini_prot = do_the_martini_thingy(prot)

system = martini_prot.createSystem(arg1, arg2, ..., argN )

...

system.steps(have_fun)

I thing many users will benefit of such a tool.

agrossfield commented 3 years ago

I might be mistaken – Justin can correct me -- but I don’t think the code is in working order at the moment.

Dr. Alan Grossfield Dept of Biochemistry and Biophysics University of Rochester Medical Center Phone: 585 276 4193 http://membrane.urmc.rochester.edu https://orcid.org/0000-0002-5877-2789 Pronouns: He/his

From: "S. CM" notifications@github.com Reply-To: maccallumlab/martini_openmm reply@reply.github.com Date: Tuesday, January 26, 2021 at 6:38 AM To: maccallumlab/martini_openmm martini_openmm@noreply.github.com Cc: Subscribed subscribed@noreply.github.com Subject: [EXT] [maccallumlab/martini_openmm] Tutorial example script? (#1)

Hello!

I am a bit new to MD, so I might be asking for something extraordinarily simple or impossible. So far I have been doing all-atom simulations with openMM in a membrane protein. They look all great, but it seems that the real interesting part happens at longer time scales.

Therefore, I am considering using trying dry Martini! I read everywhere that for long time scales, or very complex systems, coarse-grained simulations simplify the model. That saving in computing effort allows doing longer MD time. I have looked around the repository and on the web, but I could not find any "recipe-type " script. Thus, I was wondering if it would be possible to include a simple python script that would do something like:

from martini_openmm import *

prot = load_prot_and_top()

martini_prot = do_the_martini_thingy(prot)

system = martini_prot.createSystem(arg1, arg2, ..., argN )

...

system.steps(have_fun)

I thing many users will benefit of such a tool.

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHubhttps://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_maccallumlab_martini-5Fopenmm_issues_1&d=DwMCaQ&c=4sF48jRmVAe_CH-k9mXYXEGfSnM3bY53YSKuLUQRxhA&r=49qnaP-kgQR_zujl5kbj_PmvQeXyz1NAoiLoIzsc27zuRX32UDM2oX8NQCaAsZzH&m=MQYW6EkLvWD8tBekpu4Me4V3xVjgKGbfxApc6Vqpn3A&s=PIHT6czccKEyMp5syUC7zXDI0MSa4yKQbk7M4nSlagA&e=, or unsubscribehttps://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_notifications_unsubscribe-2Dauth_ADH754Q5M75P53YSROJJ7M3S32SSTANCNFSM4WTJZ5CA&d=DwMCaQ&c=4sF48jRmVAe_CH-k9mXYXEGfSnM3bY53YSKuLUQRxhA&r=49qnaP-kgQR_zujl5kbj_PmvQeXyz1NAoiLoIzsc27zuRX32UDM2oX8NQCaAsZzH&m=MQYW6EkLvWD8tBekpu4Me4V3xVjgKGbfxApc6Vqpn3A&s=W6o_em_R63feqf2BfB9Enj-fmGDYhZAxvNV1ZzZL9MI&e=.

phisanti commented 3 years ago

Mmmm, if that would be the case, do you know any other tool for running coarse-grain simulations in openMM? If possible one with for-dummies-documentation as I am fairly new in the MD word (This week will be my first Brith-month!).

Thanks in advance.

agrossfield commented 3 years ago

As far as I know, it doesn’t exist – that’s why Justin and I talked about this. The problem is that there are a couple of custom energy terms in MARTINI that don’t exist in OpenMM (at least as far as I know), and they need to be implemented before one can use OpenMM for it.

In my group, we use gromacs for our MARTINI runs. I’ve heard that NAMD supports MARTINI as well, but I haven’t tried to use it for that.

Dr. Alan Grossfield Dept of Biochemistry and Biophysics University of Rochester Medical Center Phone: 585 276 4193 http://membrane.urmc.rochester.edu https://orcid.org/0000-0002-5877-2789 Pronouns: He/his

From: "S. CM" notifications@github.com Reply-To: maccallumlab/martini_openmm reply@reply.github.com Date: Tuesday, January 26, 2021 at 7:02 AM To: maccallumlab/martini_openmm martini_openmm@noreply.github.com Cc: "Grossfield, Alan" Alan_Grossfield@URMC.Rochester.edu, Comment comment@noreply.github.com Subject: [EXT] Re: [maccallumlab/martini_openmm] Tutorial example script? (#1)

Mmmm, if that would be the case, do you know any other tool for running coarse-grain simulations in openMM? If possible one with for-dummies-documentation as I am fairly new in the MD word (This week will be my first Brith-month!).

Thanks in advance.

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phisanti commented 3 years ago

I can also give it a go at Gromacs. Do you have any tutorial or bash script that I could follow? As said before, I am fairly new in MD. The task I want to perform is fairly simple but it's long and ideally, we would run it more than once.

agrossfield commented 3 years ago

There are a bunch listed on the gromacs site. CHARMM-GUI is a good place to get the initial simulations built.

Alan

Dr. Alan Grossfield Dept of Biochemistry and Biophysics University of Rochester Medical Center Phone: 585 276 4193 http://membrane.urmc.rochester.edu https://orcid.org/0000-0002-5877-2789 Pronouns: He/his

From: "S. CM" notifications@github.com Reply-To: maccallumlab/martini_openmm reply@reply.github.com Date: Tuesday, January 26, 2021 at 7:37 AM To: maccallumlab/martini_openmm martini_openmm@noreply.github.com Cc: "Grossfield, Alan" Alan_Grossfield@URMC.Rochester.edu, Comment comment@noreply.github.com Subject: [EXT] Re: [maccallumlab/martini_openmm] Tutorial example script? (#1)

I can also give it a go at Gromacs. Do you have any tutorial or bash script that I could follow? As said before, I am fairly new in MD. The task I want to perform is fairly simple but it's long and ideally, we would run it more than once.

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agrossfield commented 3 years ago

You can check out https://www.livecomsjournal.org/article/5068-from-proteins-to-perturbed-hamiltonians-a-suite-of-tutorials-for-the-gromacs-2018-molecular-simulation-package-article-v1-0

It’s a couple of years old, but I think Justin keeps the tutorials up to date in the associated GitHub repo.

Dr. Alan Grossfield Dept of Biochemistry and Biophysics University of Rochester Medical Center Phone: 585 276 4193 http://membrane.urmc.rochester.edu https://orcid.org/0000-0002-5877-2789 Pronouns: He/his

From: "S. CM" notifications@github.com Reply-To: maccallumlab/martini_openmm reply@reply.github.com Date: Tuesday, January 26, 2021 at 7:37 AM To: maccallumlab/martini_openmm martini_openmm@noreply.github.com Cc: "Grossfield, Alan" Alan_Grossfield@URMC.Rochester.edu, Comment comment@noreply.github.com Subject: [EXT] Re: [maccallumlab/martini_openmm] Tutorial example script? (#1)

I can also give it a go at Gromacs. Do you have any tutorial or bash script that I could follow? As said before, I am fairly new in MD. The task I want to perform is fairly simple but it's long and ideally, we would run it more than once.

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phisanti commented 3 years ago

Thank you very much! I will take a look immediately.

jlmaccal commented 3 years ago

So, I'm not sure about the state of this code with OpenMM. I have not looked at this in quite some time. However, I was very close to having something completed. I implemented all of the required energy terms and developed some tests to verify that OpenMM and Gromacs give the same energy and forces to within a reasonable tolerance.

This likely needs to be cleaned up a bit and tested with the latest version of OpenMM, but this shouldn't be too hard. I also need to make sure that all of the changes I'm describing have been pushed to this repo.

Ultimately, the way I set things up, one would still need to use the same GROMACS tools to map the all atom system into a coarse grained one. The code in this repo would then be able to read in the gromacs .itp and .top files and construct the appropriate force objects.

Ultimately, I would like to finish this off and write it up as a software / tools paper (possibly for BJ). My group is just struggling to find the bandwidth to get this finished.

phisanti commented 3 years ago

@jlmaccal sounds awesome, so before I start writing with this module, do you think it would be possible to provide me with a reproducible example so that I can quickly test? Should not be to complex, just read martini files, or martinize gro files and then run a thousand of steps. One of the reasons it would be good to test is because martini allows longer time-steps, but as I am new with coarse-grain models, I don't know which scale should be right for a martini structure.

jlmaccal commented 3 years ago

@phisanti Sorry, I missed this mesage earlier.

We're focusing on getting this module into shape for publication, so there should be a lot of activity over the next month or so, including some example scripts. Stay tuned.

agrossfield commented 3 years ago

Let me know if you want a tester – we’re using gromacs for our martini runs right now, but OpenMM seems much more performant on GPUs.

Dr. Alan Grossfield Dept of Biochemistry and Biophysics University of Rochester Medical Center Phone: 585 276 4193 http://membrane.urmc.rochester.edu https://orcid.org/0000-0002-5877-2789 Pronouns: He/his

From: Justin MacCallum @.> Reply-To: maccallumlab/martini_openmm @.> Date: Wednesday, May 12, 2021 at 11:56 AM To: maccallumlab/martini_openmm @.> Cc: "Grossfield, Alan" Alan_Grossfield@URMC.Rochester.edu, Comment @.> Subject: [EXT] Re: [maccallumlab/martini_openmm] Tutorial example script? (#1)

@phisantihttps://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_phisanti&d=DwMCaQ&c=4sF48jRmVAe_CH-k9mXYXEGfSnM3bY53YSKuLUQRxhA&r=49qnaP-kgQR_zujl5kbj_PmvQeXyz1NAoiLoIzsc27zuRX32UDM2oX8NQCaAsZzH&m=1Rx8KNVCqgwy5GQmhKGVPUF4E390IVOoiXdUa2zFnN0&s=Cyco6qxlwF8eG154eBPREVe-BcBhSG22hwzBILYURxc&e= Sorry, I missed this mesage earlier.

We're focusing on getting this module into shape for publication, so there should be a lot of activity over the next month or so, including some example scripts. Stay tuned.

— You are receiving this because you commented. Reply to this email directly, view it on GitHubhttps://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_maccallumlab_martini-5Fopenmm_issues_1-23issuecomment-2D839887003&d=DwMCaQ&c=4sF48jRmVAe_CH-k9mXYXEGfSnM3bY53YSKuLUQRxhA&r=49qnaP-kgQR_zujl5kbj_PmvQeXyz1NAoiLoIzsc27zuRX32UDM2oX8NQCaAsZzH&m=1Rx8KNVCqgwy5GQmhKGVPUF4E390IVOoiXdUa2zFnN0&s=QhggQrSQQJFcbRMszopDhLPwgFz9O6fVSTsizq61ggw&e=, or unsubscribehttps://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_notifications_unsubscribe-2Dauth_ADH754TZ2ZMAIIRGMLGIXPTTNKQJZANCNFSM4WTJZ5CA&d=DwMCaQ&c=4sF48jRmVAe_CH-k9mXYXEGfSnM3bY53YSKuLUQRxhA&r=49qnaP-kgQR_zujl5kbj_PmvQeXyz1NAoiLoIzsc27zuRX32UDM2oX8NQCaAsZzH&m=1Rx8KNVCqgwy5GQmhKGVPUF4E390IVOoiXdUa2zFnN0&s=WuiIO8eRyofYeDxawSKU5UTIfy6GC922FFQBH7wAWzo&e=.

phisanti commented 3 years ago

I would be more than happy to try MARTINI on GROMACS, but my expertise lies mainly in the Python ecosystem. Do you have good tutorials to follow? My goal would be very simple, I can pre-build the membrane on CHARMM-GUI.org and then insert the membrane. After that, we just want to run the sim for enough time so that we can see some "arms" of the protein moving at different pH (we can change the protonation state of the lipid/protein for that). Do you think I could run such a system within your MARTINI-GROMACS pipeline? Otherwise, I could wait until the publication is out.

PS, I just discovered that GROMACS has been developed in the University of Groningen, where I did my masters. I worked with Prof. Oscar Kuipers (Molec. Biology), Sijbren Otto (Synth Chem) and Marco Fraaije (Enzymology). The world is so small.

jlmaccal commented 3 years ago

@phisanti We don’t have tutorials, but those should be coming. Stay tuned.

jlmaccal commented 3 years ago

@agrossfield As soon as we’re sure we have all of the potential function terms covered, we’ll be looking for testers.

agrossfield commented 3 years ago

Sounds good to me.

Dr. Alan Grossfield Dept of Biochemistry and Biophysics University of Rochester Medical Center Phone: 585 276 4193 http://membrane.urmc.rochester.edu https://orcid.org/0000-0002-5877-2789 Pronouns: He/his

From: Justin MacCallum @.> Reply-To: maccallumlab/martini_openmm @.> Date: Thursday, May 13, 2021 at 10:58 AM To: maccallumlab/martini_openmm @.> Cc: "Grossfield, Alan" Alan_Grossfield@URMC.Rochester.edu, Mention @.> Subject: [EXT] Re: [maccallumlab/martini_openmm] Tutorial example script? (#1)

@agrossfieldhttps://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_agrossfield&d=DwMFaQ&c=4sF48jRmVAe_CH-k9mXYXEGfSnM3bY53YSKuLUQRxhA&r=49qnaP-kgQR_zujl5kbj_PmvQeXyz1NAoiLoIzsc27zuRX32UDM2oX8NQCaAsZzH&m=hXqPy9NLzoqe6a3rzGFtN-9onFecedTjrjksPk21KOw&s=ikM9eIyKw5OvWtKTI-GeGB5SIb0QrlMfFQpRPmaaUmo&e= As soon as we’re sure we have all of the potential function terms covered, we’ll be looking for testers.

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