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    JUN ZHOU
    @junzhoux
    I only use pip install .
    Co Quach
    @daico007
    Can you try do pip install -e . and see if the problem persists?
    JUN ZHOU
    @junzhoux
    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
    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 ZHOU
    @junzhoux
    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 ZHOU
    @junzhoux
    @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 ZHOU
    @junzhoux
    Cool, I will try it, thanks.
    SRStead
    @SRStead
    Hello! I'm new to mosdef and MD in general -- I'm trying to use smiles code to read in the molecule I want to work with. When I visualize the molecule, everything is correct except the phenyl group geometry is off. The code I used is hba = mb.load("OC(=O)c1ccc(O)cc1", smiles=True) followed by hba.visualize(). Is this an issue with the smiles code or with the mbuild code?
    SRStead
    @SRStead
    To clarify for myself, I just tried building a cyclohexane ring using ch=mb.load("c1ccccc1", smiles=True) and it doesn't load a ring structure, just a linear chain with the first and last carbons 'bonded' by a bond extending the length of the chain.
    Co Quach
    @daico007
    Hi, I am having lunch now but I can look into your issue after that.
    Co Quach
    @daico007
    Screen Shot 2020-12-18 at 12.10.14.png
    Hi, I don't think I can replicate the issue you mentioned. The pics above is the hba structure I got using hba = mb.load("OC(=O)c1ccc(O)cc1", smiles=True).
    What version of mbuild are you using?
    SRStead
    @SRStead
    Thank you for looking into this! Good question--how can I tell? I installed recently using conda.
    Alex Yang
    @ahy3nz
    The shell command conda list | grep mbuild will tell you the version of mbuild
    SRStead
    @SRStead
    I'm running on a Windows machine; how would I check it in that case?
    Co Quach
    @daico007
    Hi, I think you should be able to type that command in the powershell terminal
    or if you are using windows linux subsystem, then that terminal should works too