Closed ricalessandri closed 1 year ago
@ricalessandri if you register here you can get a free T-shirt if you make 4 PRs in Oktober for the Hacktoberfest.
I have not looked into that (sorry, I remember about our discussions but did not have the bandwidth for that). Maybe this is a good chance. I will try to produce a plot asap.
I am however unsure whether I would really want to introduce things in this model at this point since this is the model that I have been using for the simulations.
Sure thing we just have to know if it gives an atactic or isotactic polymer. Either way is fine for me.
Finally getting to close this, some things to fix before merging so I don't forget:
Alright, I'm finally at it. This is one of the 3 things left to close this PR: tacticity. @fgrunewald we're getting atactic PTMAs, see:
Average enantiomer fractions over 100 chains of 30-mers:
enantiomer #1 : 0.39399930000000005
enantiomer #2 : 0.6059994800000001
With a 40-60% ratio. I guess this would converge to 50-50 with more (and/or longer) chains. Also, chains are not syndiotactic. I checked this by printing the dihedrals. See for yourself for the first 10 chains:
0 36.5249 | 0 36.0532 | 0 34.7708 | 0 -36.5657 | 0 35.2323 | 0 36.9282 | 0 36.1829 | 0 36.1268 | 0 -36.0353
1 34.0585 | 1 32.8891 | 1 35.7504 | 1 34.8827 | 1 38.3678 | 1 -41.1577 | 1 40.1183 | 1 -35.7562 | 1 37.7092
2 -37.2684 | 2 34.5314 | 2 -36.087 | 2 36.5295 | 2 38.1303 | 2 32.8347 | 2 37.3767 | 2 -35.1527 | 2 -39.0089
3 36.8553 | 3 34.2684 | 3 -36.7091 | 3 36.5085 | 3 -36.8466 | 3 -40.7319 | 3 35.2229 | 3 40.2213 | 3 40.0856
4 -33.6193 | 4 -32.8512 | 4 -42.2365 | 4 -37.6941 | 4 -34.7345 | 4 -37.4294 | 4 -36.0298 | 4 -36.4733 | 4 35.8881
5 37.2838 | 5 33.4698 | 5 -32.5688 | 5 37.3802 | 5 35.678 | 5 36.2165 | 5 37.1842 | 5 37.5854 | 5 -32.3946
6 35.3496 | 6 -36.0319 | 6 38.4035 | 6 39.7357 | 6 -41.5397 | 6 38.9863 | 6 40.6138 | 6 36.6165 | 6 37.2975
7 32.874 | 7 -36.0374 | 7 36.9036 | 7 36.3968 | 7 38.5483 | 7 -39.3083 | 7 -35.7891 | 7 37.9968 | 7 34.7671
8 43.9699 | 8 35.4649 | 8 -37.1433 | 8 -35.7173 | 8 37.0971 | 8 36.0991 | 8 -33.8231 | 8 31.2062 | 8 36.5176
9 35.8624 | 9 37.4412 | 9 38.3855 | 9 -39.6864 | 9 -41.669 | 9 -38.5243 | 9 38.1871 | 9 40.1058 | 9 -37.2323
10 37.6172 | 10 39.4304 | 10 34.4706 | 10 -39.4187 | 10 35.063 | 10 39.1183 | 10 33.5543 | 10 -34.6115 | 10 38.5975
11 41.7453 | 11 33.5612 | 11 35.5474 | 11 34.1137 | 11 -36.8871 | 11 35.875 | 11 -38.4814 | 11 37.2663 | 11 41.8513
12 39.0329 | 12 -34.4066 | 12 36.363 | 12 31.7394 | 12 36.6417 | 12 -35.4788 | 12 -33.0636 | 12 -35.5622 | 12 -36.0089
13 35.9318 | 13 39.8196 | 13 -39.2512 | 13 35.2016 | 13 -33.0821 | 13 -36.4384 | 13 39.1468 | 13 37.0456 | 13 36.0463
14 -34.3356 | 14 -36.6234 | 14 37.2354 | 14 39.4331 | 14 41.5223 | 14 37.71 | 14 -38.5657 | 14 37.4491 | 14 37.891
15 -34.7859 | 15 -33.715 | 15 -36.5078 | 15 -38.4706 | 15 31.7546 | 15 37.0417 | 15 36.2768 | 15 -33.8178 | 15 -37.1269
16 33.7626 | 16 -36.9238 | 16 33.5581 | 16 40.7569 | 16 36.9485 | 16 34.397 | 16 35.0809 | 16 36.8588 | 16 37.7889
17 39.1062 | 17 38.5846 | 17 33.7556 | 17 38.6473 | 17 37.9576 | 17 36.227 | 17 33.3178 | 17 38.425 | 17 36.5993
18 -36.0831 | 18 33.9731 | 18 -39.3478 | 18 -36.6049 | 18 -35.2307 | 18 -35.9973 | 18 33.6778 | 18 38.6039 | 18 34.586
19 -32.5932 | 19 -34.7784 | 19 -34.793 | 19 -34.527 | 19 38.7232 | 19 -33.607 | 19 33.8859 | 19 35.1522 | 19 -35.5263
20 -39.7191 | 20 38.3118 | 20 35.6131 | 20 36.365 | 20 37.1533 | 20 39.9286 | 20 37.0797 | 20 -36.2315 | 20 36.6258
21 39.7267 | 21 39.9699 | 21 38.0917 | 21 37.1777 | 21 -42.0094 | 21 36.3877 | 21 -36.6893 | 21 -36.845 | 21 -34.415
22 34.2142 | 22 36.3733 | 22 35.9077 | 22 -35.3277 | 22 36.8763 | 22 36.5706 | 22 36.445 | 22 -33.9113 | 22 40.454
23 -39.275 | 23 37.1109 | 23 -37.8667 | 23 38.5636 | 23 -35.4948 | 23 -39.1039 | 23 36.604 | 23 34.715 | 23 -35.9212
24 36.3931 | 24 37.9223 | 24 37.0983 | 24 37.749 | 24 -33.4265 | 24 35.8632 | 24 -37.5184 | 24 36.9496 | 24 -38.328
25 -34.1988 | 25 -39.3313 | 25 38.5158 | 25 37.0989 | 25 -37.5111 | 25 37.9106 | 25 36.1155 | 25 -38.0322 | 25 38.8457
26 34.4993 | 26 29.5963 | 26 -35.9228 | 26 37.5261 | 26 36.3587 | 26 37.3568 | 26 -37.3268 | 26 -35.1047 | 26 39.0637
27 33.1792 | 27 35.752 | 27 -37.0754 | 27 -38.6848 | 27 37.4816 | 27 -35.7833 | 27 38.576 | 27 -34.3623 | 27 37.3753
28 -34.6558 | 28 42.5101 | 28 -40.0315 | 28 37.6345 | 28 -38.7036 | 28 35.2331 | 28 -39.6963 | 28 37.8905 | 28 32.9077
29 31.8568 | 29 31.8861 | 29 40.188 | 29 -37.5955 | 29 33.4013 | 29 -38.7681 | 29 -36.739 | 29 37.571 | 29 38.1437
Not sure if you want this more quantitative. In case, what's a smart metric for this?
I resolved the previous issues. I also added a test: 2e207a3. It seems to be working.
I guess this is ready to be merged, @fgrunewald .
One test fails but I think it's not related to this .ff file. EDIT: I re-triggered and all is fine.
@ricalessandri you can also consider adding a line on the news section of the readme file to promote your paper
Thanks for the nice ideas!
I've added the warning, it works: https://github.com/marrink-lab/polyply_1.0/blob/006e37ed44d2f8730e806cd66d5de8b71c4859f0/polyply/data/oplsaaLigParGen/links_PTMA.ff#L164-L174
I didn't include that [ non-edges ]
sections of P3HT, which would have looked like this:
[ link ]
[ atoms ]
C01 {"resname": "PTMA"}
[ warning ]
You should patch PTMA with a CH3-terminal residues. Use -seq CH3a:1 PTMA:4 CH3b:1
[ non-edges ]
-C1 C01
-C17 C01
[ link ]
[ atoms ]
C17 {"resname": "PTMA"}
[ warning ]
You should patch PTMA with a CH3-terminal residues. Use -seq CH3a:1 PTMA:4 CH3b:1
[ non-edges ]
C17 +C1
C17 +C01
because it didn't make any difference in the resulting itp
and I wasn't sure about their purpose. Let me know if it should be there.
As a side note, I played with the behavior and the warnings will be printed twice for each residue (i.e., 8 times for PTMA:4
). While the twice is fine because it's one for CH3a and one for CH3b, printing it for each residue seems unnecessary. Also, if I use: PTMA:4 CH3b:1
or CH3a:1 PTMA:4
I was expecting polyply to print only one warning, but it still prints two. Let me know if there's something wrong with my definitions. Otherwise, these are anyway minor things because we want the user to use CH3a:1 PTMA:4 CH3b:1
anyway.
I will include the news piece in the other PR later today.
@ricalessandri the non-edges are specifically to reduce the number of warnings being printed and in principle, you could even use them to specifically target only one end, like if you miss CH3b it would only do 1 warning. However, there is a small syntax mistake in the non-edges of the first residue. It should first mention the atom that is also in the atoms directive. So it should be:
[ link ]
[ atoms ]
C01 {"resname": "PTMA"}
[ warning ]
You should patch PTMA with a CH3-terminal residues. Use -seq CH3a:1 PTMA:4 CH3b:1
[ non-edges ]
C01 -C1
C01 -C17
If you adjust this, the PR should be ready to go.
@fgrunewald done! I implemented and tested and works as expected (1 warning for CH3a if I miss that, 1 warning for CH3b if I miss that, of 2 warnings if I miss both) - fantastic!
PR for contributing the OPLS-based AA FF developed for PTMA in https://arxiv.org/abs/2209.02072.
I will shortly add a test. Also open a separate PR to contribute CG model(s).