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chamikaradk / Polymer-ITP-generator

Generate automated initial topology for gromacs simulations
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pairs interactions for polymer chains #1

Open yel21 opened 5 months ago

yel21 commented 5 months ago

Hello!

I appreciate your script.

I am attempting to use the ITP_Gen_V9_newparams.ipynb program to create polymer chains specifically for PET (polyethylene terephthalate).The monomer unit's characteristics were acquired using libpargen, while the partial charges were computed using quantum chemistry.

Can you clarify the process by which you create [pairs] interactions for your polymer chains?

Sincerely, Victor

chamikaradk commented 5 months ago

Thanks for using the code. I do not generate pairs in this case, as I can let GROMACS automatically generate them set this way under gen pairs [ defaults ] ; nbfunc | comb-rule | gen-pairs | fudgeLJ | fudgeQQ 1 | 2 | yes | 0.5 | 0.8333

yel21 commented 5 months ago

Hello!

Recently, we conducted an examination of the status of 1-4 interactions in Gromacs. Kindly refer to the discussion found at this link: [[gmx-users] 1-4 LJ interactions] (https://www.mail-archive.com/gromacs.org_gmx-users@maillist.sys.kth.se/msg40932.html) The link provided is from the Mail Archive of the gromacs.org_gmx-users mailing group. The issue lies in the insufficiency of generating 1-4 parameters that are absent in the pair list from regular Lennard-Jones parameters using fudgeLJ. To verify this, you may just examine the gmx dump of your tpr file and inspect the lines containing the functype[6]=LJ14 designation. Hence, it is insufficient to only provide "gen pairs = yes" in the [default] parts of the itp file. The [pairs] sections must also be explicitly included.

Sincerely, Victor

chamikaradk commented 5 months ago

Interesting! However, as mentioned in the thread you provided, Urea does not have 1-4 intramolecular interactions. And any 1-4 interaction containing H atoms does not count as H is considered too small to interact 3 bonds apart. You may want to test using a better example (ex. butane) to be sure about this

yel21 commented 5 months ago

Actually, We found this on the n-eicosane. The results were rather different in one case. https://pubs.rsc.org/en/content/articlehtml/2020/ra/d0ra90087g. . It is interesting, how it will be for your systems.