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    ramanishsingh
    @ramanishsingh
    Thanks @mikemhenry . md works much better. The initial structure has much lower ene
    *energy as compared to steep and cg
    Mike Henry
    @mikemhenry
    Glad that worked for you @ramanishsingh
    ramanishsingh
    @ramanishsingh

    How to install mbuild on cluster?
    I tried : python -m pip install --user mbuild
    but when I import mbuild it gives me an error:

    Traceback (most recent call last):
    File "<stdin>", line 1, in <module>
    File "/panfs/roc/groups/12/siepmann/singh891/projects/signac/mnd/mbuild/mbuild/init.py", line 2, in <module>
    from mbuild.coarse_graining import coarse_grain
    File "/panfs/roc/groups/12/siepmann/singh891/projects/signac/mnd/mbuild/mbuild/coarse_graining.py", line 3, in <module>
    from mbuild.compound import Compound
    File "/panfs/roc/groups/12/siepmann/singh891/projects/signac/mnd/mbuild/mbuild/compound.py", line 14, in <module>
    import mdtraj as md
    File "/home/siepmann/singh891/.local/lib/python3.7/site-packages/mdtraj/init.py", line 30, in <module>
    from .formats.registry import FormatRegistry
    File "/home/siepmann/singh891/.local/lib/python3.7/site-packages/mdtraj/formats/init.py", line 4, in <module>
    from .dcd import DCDTrajectoryFile
    File "init.pxd", line 918, in init mdtraj.formats.dcd
    ValueError: numpy.ufunc size changed, may indicate binary incompatibility. Expected 216 from C header, got 192 from PyObject

    Alex Yang
    @ahy3nz
    It looks like the issue is with the mdtraj library. How did you install mdtraj?
    ramanishsingh
    @ramanishsingh
    python -m pip install --user mdtraj
    Justin Gilmer
    @justinGilmer

    Sorry just getting to this @ramanishsingh . To install mbuild on a cluster, we recommend using Anaconda to install and create an environment. We host mBuild and Foyer to be pip installable, however, some of our dependencies like mdtraj do not list all of their dependencies like numpy with their pip recipe.

    It is usually a much easier process to install through anaconda.

    conda create -n mosdef36 python=3.6
    conda activate mosdef36
    conda install -c mosdef -c conda-forge -c omnia mbuild foyer

    If you do not have anaconda on the cluster, you can download a minimial conda install called miniconda

    https://docs.conda.io/en/latest/miniconda.html

    ramanishsingh
    @ramanishsingh
    Do I need to install open babel separately?
    I tried installing it from pip and source but couldn't get it installed.
    Justin Gilmer
    @justinGilmer

    that can also be installed using conda

    conda install -c openbabel openbabel

    ramanishsingh
    @ramanishsingh
    The conda install is also not working,
    "'An unexpected error has occurred. Conda has prepared the above report.
    If submitted, this report will be used by core maintainers to improve
    future releases of conda."
    Justin Gilmer
    @justinGilmer
    when trying to install conda? or when trying to install mbuild
    ramanishsingh
    @ramanishsingh
    Sorry for the vague message.
    Conda is already installed on the cluster, and I successfully installed mbuild using the commands you posted.
    But open babel installation is not working, with : conda install -c openbabel openbabel
    or pip install
    Justin Gilmer
    @justinGilmer

    Hmm,

    There are a few other channels you can try to install it from:
    conda install -c bioconda openbabel
    conda install -c conda-forge openbabel

    if those do not work, you might need to contact the IT department of the cluster and see if they can help.

    Alyssa Travitz
    @atravitz
    hi all, i'm trying out mbuild today and wanted to know if there's a way to add constraints to packing. I typically use the select atom function in packmol, and don't see an analogous method in mbuild. I want to essentially have a layer of molecules with their 'ports' all arranged on an invisible surface. i know that monolayer exists, but it looks like i'd need to explicitly define a lattice layer for a surface?
    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 ZHOU
    @junzhoux
    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 ZHOU
    @junzhoux
    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 ZHOU
    @junzhoux
    @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 ZHOU
    @junzhoux
    I only use pip install .