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Discussion/Questions for all things MoSDeF (mosdef.org)

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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line 26, the call for TiledCompound is outdated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 .

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

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 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

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

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