Sang nanoparticle

[MDSYN2019]

Apologies for the delay. Have been rather busy lately. Created first version of the nanoparticle generator. Some notes:

• I've made a PCBM-fullerene nanoparticle with it that adapts a custom vermouth interaction between the CBM and the phenyl group, but this can be replaced with more accurate values. The nanoparticle at the moment adopts the Monticelli model for C60, and ligparm generator with the OPLS FF.

• I have included the nanoparticle_generator.py code in the src folder, as well as the sample itp files made from it, and the topology I made with the files. The minimized structure of the nanoparticle is also included there.

• The 'Janus' and 'Striped' options do the same thing as none at the moment - this should be expanded soon

• I will be adding a 'generic' core generator with this with the next pull request, to adapt making a generic fibanocci sphere with custom constraining bonds

• The idea with gold nanoparticles eventually is to add the core as available libraries of cores, where we can attach different types of ligands onto these spheres.

• Generating unit cell type nanoparticles for this module is another thing I will be working on for the next iteration.

Please let me know if you need more information.

[fgrunewald]

@Shtkddud123 thanks for removing the files. Can you also run a 'git rebase master'. That should take care the files are wiped from the record, while keeping all the changes.

[MDSYN2019]

Hi Fabian.

I've rebased the repo. Please let me know if there are issues!

Thanks

Sang

On Sat, Jan 14, 2023 at 8:29 PM Fabian Grunewald @.***> wrote:

@Shtkddud123 https://github.com/Shtkddud123 thanks for removing the files. Can you also run a 'git rebase master'. That should take care the files are wiped from the record, while keeping all the changes.

— Reply to this email directly, view it on GitHub https://github.com/marrink-lab/polyply_1.0/pull/286#issuecomment-1382909560, or unsubscribe https://github.com/notifications/unsubscribe-auth/ALDTKNMATVTPANOOCE7WNSDWSMEBTANCNFSM6AAAAAASOLHDIM . You are receiving this because you authored the thread.Message ID: @.***>

[fgrunewald]

@MDSYN2019 awesome! you also need to push the rebase

[Shtkddud123]

Hi Fabian,

I think I did push it? Please let me know if there are issues. My apologies

• not used to rebase as I've always had a warning in my head only to use it in desparate circumstances!

Thanks

Sang

On Sun, Jan 15, 2023 at 6:56 PM Fabian Grunewald @.***> wrote:

@MDSYN2019 https://github.com/MDSYN2019 awesome! you also need to push the rebase

— Reply to this email directly, view it on GitHub https://github.com/marrink-lab/polyply_1.0/pull/286#issuecomment-1383224878, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABED7FBRVBG2LBA2TTEREMDWSRB6ZANCNFSM6AAAAAASOLHDIM . You are receiving this because you were mentioned.Message ID: @.***>

[fgrunewald]

@MDSYN2019 sorry something is still amiss; it seems the build directory is still part of the PR.

@pckroon removing the superfluous files and doing a git rebase should have solved the problem no?

[Shtkddud123]

Hi Fabian,

I will have another look today. I will also push whatever progress I've made regarding the NP cores processor today as well.

Best wishes

Sang

On Thu, Jan 19, 2023 at 8:54 AM Fabian Grunewald @.***> wrote:

@MDSYN2019 https://github.com/MDSYN2019 sorry something is still amiss; it seems the build directory is still part of the PR.

@pckroon https://github.com/pckroon removing the superfluous files and doing a git rebase should have solved the problem no?

— Reply to this email directly, view it on GitHub https://github.com/marrink-lab/polyply_1.0/pull/286#issuecomment-1396635416, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABED7FDTUUF54G23B3BDIFTWTD6MVANCNFSM6AAAAAASOLHDIM . You are receiving this because you were mentioned.Message ID: @.***>

[pckroon]

@pckroon removing the superfluous files and doing a git rebase should have solved the problem no?

Not 100% sure, but I think you need to do git rebase -i, and drop/modify the commit that adds the problematic file(s), and then force push

[fgrunewald]

@Shtkddud123 I just saw that the rabase has worked! Nice job. There is, however, one more thing which has to go. You're also pushing the 'build' folder. That is your local installation of polyply but should not part of the PR. Removing it the same way as the other files should to the trick.