Sang nanoparticle #286

MDSYN2019 · 2022-11-29T11:10:12Z

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

This already looks like a very good draft! I've added a bunch of comments in order to reshape the organization such that it fits in better with the rest polyply, eventually.

However, to make faster progress and start testing I recommend the following: Try to create a function gen_np that essentially generates coordinates and itp files for nanoparticles with a signature similar to gen_coords and gen_itp. We worry later on how to integrate that with the rest of the functions. In my last review comment I've drafted what such a function could look like in general.

In addition to creating this function I would recommend two other objectives for now:

Let's try to externalize data-files for the core and ligands as well as links into the libraries in form of .ff files. In the review I've made some comments on how to do that.
Let's try to split parameter generation and coordinate generation into three processors.

a) First let's try have one Processor for making the core coordinates. See my comment on line 81ff for what I would propose.
b) Then let's have a a Processor, which does the ligand attachment on the graph but doesn't generate coordinates (i.e. everything that is related to _convert_to_vermouth_molecule) BUT give it the core coordinates in form of a molecule from the previous step. see comment for more details.
c) Finally we have processor that generates only the coordinates for the ligand attachment. This is not yet implemented as far as I can see, is that right?

polyply/src/nanoparticle_constructor.py

fgrunewald · 2023-01-14T20:29:02Z

@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 · 2023-01-15T18:20:40Z

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 <#286 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ALDTKNMATVTPANOOCE7WNSDWSMEBTANCNFSM6AAAAAASOLHDIM> . You are receiving this because you authored the thread.Message ID: ***@***.***>

fgrunewald · 2023-01-15T18:56:34Z

@MDSYN2019 awesome! you also need to push the rebase

Shtkddud123 · 2023-01-15T19:34:41Z

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 <#286 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABED7FBRVBG2LBA2TTEREMDWSRB6ZANCNFSM6AAAAAASOLHDIM> . You are receiving this because you were mentioned.Message ID: ***@***.***>

fgrunewald · 2023-01-19T08:54:23Z

@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 · 2023-01-19T10:13:51Z

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 <#286 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABED7FDTUUF54G23B3BDIFTWTD6MVANCNFSM6AAAAAASOLHDIM> . You are receiving this because you were mentioned.Message ID: ***@***.***>

pckroon · 2023-01-23T13:12:54Z

@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

… morse force field parameters with it

fgrunewald · 2023-02-01T12:01:01Z

@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.

fgrunewald

Hi Sang,

I was doing some reviewing in different PRs, so I added some comments here as well. Note I did not do an extensive review though, just some suggestions here and there.

Please note implementing the ApplyLinks usage will require to write ff files with links. If you get to that point let me know, because you'll probably need some pointers.

Good job so far!
Fabian

fgrunewald · 2023-02-07T13:49:51Z

polyply/data/nanoparticle_test/AMBER_AU/au102.gro

@@ -0,0 +1,105 @@
+generated by VMD, t= 0.000000


this file should live in 'polyply/tests/test_data'

fgrunewald · 2023-02-07T13:50:08Z

polyply/data/nanoparticle_test/AMBER_AU/au144.gro

@@ -0,0 +1,147 @@
+generated by VMD, t= 0.000000


same as before move this to tests/test_data

fgrunewald · 2023-02-07T13:52:42Z

polyply/data/oplsaaLigParGen/C60.ff

+; ----------------------------------------------------------------------------
+;   Topology for C60 fullerene
+;   Luca Monticelli, December 2007
+;   If you find this useful, please cite: 
+;   Monticelli L., J. Chem. Theory Comput. 2012, 8, 1370-1378
+; ----------------------------------------------------------------------------
+;  - Geometry from NMR data  
+;    (Yannoni et al, J. Am. Chem. SOC. 1991, 113, 3190-3192)
+;
+;  - Atom type CFUL: from Girifalco, J. Phys. Chem. (1992),96, 858-861
+;
+;  - Bond and angle parameters:
+;    same as for CA-CA (and CA-CA-CA) in OPLS-AA (CA is the aromatic carbon)


FYI for later: citations can be added to .ff files using the [citations] directive. It requires there to be a .bib file with the actual citations and the key provided in the directive to be the same as in the bibtex file. Also by convention the .bib file needs to have google-scholar format, which is comma separated entries.

fgrunewald · 2023-02-07T14:14:24Z

polyply/src/nanoparticle_constructor.py

+    system = np_top.convert_to_vermouth_system()
+    NanoparticleLigandCoordinates().run_system(system)


instead of this, you can provide the np_top to generate templates like so:

# this line is needed in order for it to skip generation of the core coordinates. full_np_metamol.templates = {"rename of core": core coordinates} LigandGenerator = GenerateTemplates(topology=np_top, max_opt=10).run_system(np_top)

This will generate all Ligand coordinates, which can be accessed through full_np_metamol.templates

fgrunewald · 2023-02-07T14:16:38Z

polyply/src/nanoparticle_constructor.py

+        self.meta_mol.molecule = self.np_molecule
+        return self.meta_mol
+
+    def create_itp(self, write_path):


this function is not needed. Processors just return molecules. I/O is handled at the level of gen_np

fgrunewald · 2023-02-07T14:16:58Z

polyply/src/nanoparticle_constructor.py

+        with open(str(write_path), "w") as outfile:
+            write_molecule_itp(self.np_molecule, outfile)
+
+    def create_gro(self, write_path):


same as above I/O should be handled on the level of gen_np

fgrunewald · 2023-02-07T14:23:29Z

polyply/src/nanoparticle_constructor.py

+        for index, index2 in enumerate(
+            list(core_index_relevant.keys())[: self.ligands_N]
+        ):
+            interaction = vermouth.molecule.Interaction(
+                atoms=(index2, attachment_list[index] + attachment_index),
+                parameters=["1", "0.0033", "50000"],
+                meta={},
+            )


I understand that this is just a draft. I'll add a comment anyways ;) If you only add an edge between the ligand and the core nanoparticle using molecule.add_edge, we can in a later step run ApplyLinks to get the bonded interactions straight from the force-field files. This will make it easier to adopt them later.

So my suggestion:

np_molecule.add_edge(index2, attachment_list[index] + attachment_index)

Then run ApplyLinks() from polyply.src.apply_links in line 251

fgrunewald · 2023-02-07T14:24:52Z

polyply/src/nanoparticle_constructor.py

+        for node in self.np_molecule.nodes:
+            # change resname to moltype
+            self.np_molecule.nodes[node]["resname"] = "TEST"


This is dangerous. I would suggest the core to have the same rename but keep the ligand resname. We need to pay some attention though later when running the ApplyLinks

…e and PCBM

…ork on the AA PCBM example

Shtkddud123 added 2 commits November 29, 2022 11:02

added PCBM-fullerene generation code with the polyply branch

acf0495

added PCBM-fullerene generation code with the polyply branch

cfff153

fgrunewald requested changes Dec 5, 2022

View reviewed changes

Shtkddud123 added 4 commits January 5, 2023 12:35

updated much of the functions as required - further changes to be made

2ad2fdf

added new functionalities to ensure gro files are correctly generated

1fb9868

removed some datetime libraries not being utilized

c6bfecc

removed . files that are too large!

3ce1d3a

removed notebook

949fbe1

Shtkddud123 added 4 commits January 28, 2023 15:26

rebased and forced push

47cc745

rebased and forced push

1dfa72d

added basic lattice generator

6e4ed35

very basic gold lattice generation now works - but need to add in the…

2d8804e

… morse force field parameters with it

removed build

04305f9

fgrunewald reviewed Feb 7, 2023

View reviewed changes

Shtkddud123 added 8 commits March 3, 2023 19:35

added new nanoparticle part

67b8afd

added additional ligand compatibility

b5a2e50

removed some extraeous files

8f78896

new

dab2e43

nearly fixed force field issue..

f42c1be

modified the bond adder to make it work

9bdc2c6

modified the bond adder to make it work

cd6dd70

more progress - need to fix key issues

ae6620c

Shtkddud123 added 30 commits June 6, 2023 21:45

making PCBM NP

b562afe

added PCBM model

be460b0

A version of PCBM model working..

7a97aec

fixed the rotation matrix - should work now for both gold nanoparticl…

65a7572

…e and PCBM

still need to fix smaller points, but overall in good shape. Now to w…

76de52b

…ork on the AA PCBM example

fixed weird issue with the PCBM ligand

1f7925f

changed some docstrings for the nps

fea287f

removed code that were not required anymore

fc03adb

shorted some of the pattern recognition to a single function

ab9b8ff

Adding some new generic nanoparticle creation functions

c69a902

fixing some inner ligands placement inside core

28d3a90

still not perfect but updated

12df3d1

progress on generic NP object

bb6d5fd

moved generic gold nanoparticle class to nanoparticle_generic

a78504a

new

23f79f5

new

9dfc31d

new

2952955

updated nanoparticle generic

1a49794

made more modifications

7c6e79a

updated

864305b

added python 2 function

5c9e8c5

fixed more parts

b1c2552

fixed itp issue again

0859812

modified the artificial core generation code

4702bc4

fix: more changes

5ac47e6

added martini3 small molecules to work with articifical NPs

dd23bd5

new: added new modules

eb5b00e

fixed weird issue

07aeadb

corrected bond generator

2829c37

new

bb4bc6e

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Sang nanoparticle #286

Sang nanoparticle #286

MDSYN2019 commented Nov 29, 2022

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fgrunewald commented Jan 14, 2023

MDSYN2019 commented Jan 15, 2023 via email

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Shtkddud123 commented Jan 15, 2023 via email

fgrunewald commented Jan 19, 2023

Shtkddud123 commented Jan 19, 2023 via email

pckroon commented Jan 23, 2023

fgrunewald commented Feb 1, 2023

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fgrunewald Feb 7, 2023

fgrunewald Feb 7, 2023

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fgrunewald Feb 7, 2023

fgrunewald Feb 7, 2023

fgrunewald Feb 7, 2023

		system = np_top.convert_to_vermouth_system()
		NanoparticleLigandCoordinates().run_system(system)

Sang nanoparticle #286

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Sang nanoparticle #286

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