Where communities thrive


  • Join over 1.5M+ people
  • Join over 100K+ communities
  • Free without limits
  • Create your own community
People
Activity
    Matt Thompson
    @mattwthompson
    Hi Alyssa, there are probably a few different ways of handling this, not sure which is best. One that comes to mind is initializing a 2-D lattice and populating compounds out in those two dimensions. This would produce an ordered structure (I don't know if that's good or bad for your use case) but it would assure that the ports are pointing in the same way.
    If you wanted to go with a packing approach to get a less-ordered initial structure, we don't have the atom selection syntax built in at the moment but I think @mikemhenry has accomplished similar things by using the fix_orientation flag that prohibits rotation while packing
    Alyssa Travitz
    @atravitz
    i'm avoiding an ordered structure if possible, @mikemhenry 's solution sounds like it would work. my ideal case would be putting bounds on the 'ports', similar to atom selection, but I'll try fix_orientation and let you know how it goes :)
    Mike Henry
    @mikemhenry
    Good luck @atravitz maybe it would work if you do the rotations to get things aligned the way you want them to, then to use fix_orientation also if there is some functionality you want extend to mbuild's packmol wrapper, let me know!
    Alyssa Travitz
    @atravitz
    thanks @mikemhenry. I'd like to extend mbuild's packmol wrapper. who would be the right person to talk to about the "right" way to go about it? I have a few ideas of how to implement it, but I want it to be as friendly/similar to your api as possible
    Justin Gilmer
    @justinGilmer

    @atravitz our resident expert is @mattwthompson but myself and a few others have played around with its api as well.

    So if you want to start a discussion on GitHub, that would probably get a lot of good input!

    ramanishsingh
    @ramanishsingh
    Hi, this may be a very stupid question, but is there a simple way to do a very basic MD simulation (maybe using GAFF) after generating the input structure using mbuild?
    ramanishsingh
    @ramanishsingh
    I mean what would be the easiest and fastest option.
    I will be using the structure generated by mbuild for CP2K MD, so want to run a few MD steps using a FF before I throw that structure in CP2K.
    Matt Thompson
    @mattwthompson
    The general strategy would be to write it out to an MD engine and use update_coordinates against the output file
    you could run something in LAMMPS or GROMACS with a simple input script
    ramanishsingh
    @ramanishsingh
    Thanks Matt.
    I have more questions.
    currently I am generating the .top file using self written xml file.
    Is there any way I can generate the .top file using 'GAFF' or 'oplsaa' without having to write the xml file? ( I am also doing the energy minimization using GAFF and I think that uses Openbabel)
    forcefield_name='oplsaa' is giving me this error:
    AttributeError: 'Atom' object has no attribute 'whitelist'
    Matt Thompson
    @mattwthompson
    That error usually means the force field object is empty
    try Forcefield(name='oplsaa')
    ramanishsingh
    @ramanishsingh
    That works!! thanks
    Bradley Dice
    @bdice
    Hi all, does MoSDeF have a logo? I didn't see anything besides plain text "MoSDeF" on the website, and just wanted to be sure I wasn't missing anything when I give MoSDeF credit.
    Matt Thompson
    @mattwthompson
    One is in the works, hopefully won't be long now
    Bradley Dice
    @bdice
    @mattwthompson Cool! Let me know when it's done. We also have a new logo for signac in the works, we'll share that with you too.
    Bradley Dice
    @bdice
    Thanks for the stickers!
    Matt Thompson
    @mattwthompson
    🔥🔥🔥
    Peter T. Cummings
    @ptc2ug
    I came here from mosdef.org by clicking the chat button
    cool
    Mike Henry
    @mikemhenry
    Welcome :wave:
    jun
    @Heyjunzhou
    Hi all, when I try to run the Example4 in /nanoparticle_optimization/tutorial, why I get a error message "module 'mbuild' has no attribute 'TiledCompound'"?
    Co Quach
    @daico007
    Hey @Heyjunzhou, can you throw me the link to that repository?
    Never mind, I found that repo. The internal recipes of mbuild have been moved around sometime ago and might causes the above issue. I update the import path and hopefully resolve that issue.
    jun
    @Heyjunzhou
    Hi, thanks for your reply. So that means I need to reinstall the mbuild? Actually I have try this, but the error still occurs. I also tried other three tutorial files, all work well.
    Co Quach
    @daico007
    I am looking into the problem now. In nanoparticle_optimization/nanoparticle_optimization/lib/nanoparticles/AA_nano.py, line 26, the call for TiledCompound is outdated
    The temporary fix for this error is to change mb.TiledCompound to mb.recipes.TiledCompound
    I will try to update this repo to work with the new mbuild version
    Then you will only need to reinstall this repo (reclone it and do the pip install), you will not need to reinstall the main mbuild package
    jun
    @Heyjunzhou
    @daico007 , thanks, I also noticed that the Tiledcompound has been moved to the mbuild/lib/recipes, so I have tried to modified mb.TiledCompound to mb.lib.recipes.TiledCompound or mb.recipes.TiledCompound as you suggested. Still not work. Maybe I need to wait for your updates, thanks for your help.
    Co Quach
    @daico007
    did you do pip install -e . or just pip install .?
    And have you tried restart the kernel with the notebook after making those changes?
    jun
    @Heyjunzhou
    I only use pip install .
    Co Quach
    @daico007
    Can you try do pip install -e . and see if the problem persists?
    jun
    @Heyjunzhou
    Thanks, it works now.
    When I read the original paper of Mbuild, there is a example showing how to tether PEG chains to a silica nanoparticle. Why in new verson it seems that this has been removed?
    Co Quach
    @daico007
    I think you are referring to our tnp recipes (correct me if I am wrong) which have been recently moved to a new repo
    https://github.com/mosdef-hub/mbuild-examples/tree/master/tnp
    The main reason we moved these recipes/examples to a different repo is that we try to keep the main mbuild package lightweight and only contains the core structures and functionalities
    The tnp, as well as some other recipes, is more in-depth, and is usually used an example of what mbuild can do. So we decided to migrate them to a separate repo and only keep the core features in the main mbuild package.
    jun
    @Heyjunzhou
    Thanks for your reply, but this is not what I want. In Chapter 5 of this book (10.1007/978-981-10-1128-3), which introduce the Mbuild tool. There is a example in Page 84, fig 4 to show how to use mbuild to show how to modify the surface of a spherical nanoparticle. This is very similar to another example called 'alkane_monolayer’. I am just wonder why this do not included in the example file, if possible, would you please provide it to me. Thanks.
    Co Quach
    @daico007
    I will try to find that specific example and notify you once I found it.
    Co Quach
    @daico007
    Hey @Heyjunzhou, I updated the nanoparticle_optimization repo to work with the current version of mbuild (I think you can either do a git pull or reclone the repo) .
    About the example you pointed out, it seems like a modification of the tnp class (the one on the link above) with the Silica nanoparticle and PEGSilane chain.
    I can try recreate that example and put it in a jupyter notebook and send it to you in the next few days (hopefully tomorrow)
    jun
    @Heyjunzhou
    @daico007 Thank you very much. It works all well now.
    Co Quach
    @daico007
    Hi @Heyjunzhou , I made a silica tnp (with pegsilane chains) example, which can be found here: https://github.com/daico007/TNP.
    Please let me know if you have any problem with the repo (or any question in general ).
    jun
    @Heyjunzhou
    Cool, I will try it, thanks.