Replies: 21 comments
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Dear @WeixZeng, Let's say you have 100 residues each the syntax would be as follows:
The connect is interpreted as follows: Take seq block 0 ( i.e. A) and connect it to block B (i.e. 1) by putting a bond between residues 0 and 99. All counts are zero-indexed (i.e. first residue has resid 9 and 100 residues have a resid of 0 to 99). Now you can generate a GROMOS itp file using:
We also have set up (but not released) a workflow to generate itp files for other force fields like OPLS or CHARMM36 for which monomers are not part of the library yet. Depending on your problem it might be more appropriate to use these force fields. Let me know if you are interested and I will show you how to set up those polymers. |
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Hi @fgrunewald , I tried workflow you taught. It works well and can generate .gro file for the target polymer melt, but I also found some problems with the coordinates.
Many thanks! |
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Hi @WeixZeng,
Can you try? If you decide to work with OPLS instead I'm sure @ricalessandri can help setting up the parameters. |
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Hahh, thank you for your patience. I will try it right away. Yes, I would like to work with OPLS maybe after working out my current issues and graduate from beginner period. |
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@WeixZeng ok! I'll organize the parameters |
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Yes, I can help with OPLS. Feel free to ping me here when it's time. |
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@fgrunewald Thank you! The chains bacame much nicer after the EM process. @ricalessandri Could you please share the workflow for genertating itp files with OPLS? Many thanks! |
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I checked a bit the tutorials, and found there's '1. oplsaaLigParGen' in the library list, but it only contains a few blocks at current version. If I understood the workflow correctly, to generte an itp file with OPLS-AA forcefield, it needs parameters of the blocks. Therefore, I should write the parameters first. I actually also need to set up relevant coarse-grained polymer model and tried to follow provided tutorials, felt it quite good to simply switch a library with the gen_params function that generating itp files in different scale with the same .json sequence description. I tried to generate the same block copolymer melt with Martini3 force field with following protocal:
with top file as: [ molecules ]
But it run into an OSError says: Could you please help to figure out the problem here? Many thanks! |
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I'm sorry, I have been travelling but I should be able to reply to you
today or max tomorrow.
|
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No worries and no hurry at all. Do take your time and enjoy your trip! For the AA model, if oplsaaLigParGen is the right library, it would be great to share the workflow to write .ff file for a PMMA monomer with the chiral and the link site information as an example. Cheers, |
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Hi @WeixZeng, sorry, it's been busier than expected (and Fabian is on vacation). [ Martini 3 ]
PS block and links:
And the PS-PMMA link:
Just note that we use this nomenclature, so you need to use "MMAC" and "STYR" instead of "PMMA" and "PS":
Let me know if something isn't clear. I will soon share the OPLS parameters. |
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@WeixZeng You can find OPLS parameters for PMMA: https://github.com/marrink-lab/polyply_1.0/pull/360/files |
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Thank you @ricalessandri. Really helpful! About the Martini 3. Looks like the main differences comparing with those in current library are the resname and the link connecting. Sorry, I'm still quite new at polyply either Martini, but how could I update the library (maybe at my local server) or use the new connecting parameters to generate input file with polyply? About the OPLS-AA. I'm working on PMMA-PS system currently and might need to build some new monomer in the future, don't need PMA at this stage. I'll try a bit to figure out how to generate OPLS-AA .ff file for PS refering to the PMMA parameters you shared. Considering your development progress, it would be great if you could also share the OPLS model for PS. |
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Regarding Martini 3, if you put all the lines I posted above from:
to:
in one file, say
Note that I replaced the Regarding OPLS, I'll share PS, too, then. And I will keep you posted on updates on the development. |
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@WeixZeng you can find the PS .ff OPLS file at https://github.com/marrink-lab/polyply_1.0/pull/361/files |
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@ricalessandri Then the question is to build PS/PMMA copolymers, thought the main thing needed is the PS-PMMA link. I tried to write with the OPLS .ff files you shared, while the vinyl carbons changed to VC1 and VC2, i.e. in PS, C08→VC1 and C01→VC2; and in PMMA, C01→VC1, C02→VC2, the link parameter as follows:
then tried use similar workflows as the UA or Martini3 forcefield, but doesn't work. The OPLS-AA forcefield used here was the OPLS-AA/M obtained from Jorgensen group's officail website: https://traken.chem.yale.edu/doc/GMX_OPLSAAM.zip Could you please help to check the PS-PMMA link and if the OPLS-AA forcefield is the right version, considering the PS and PMMA parameters you shared. Many thanks. |
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@WeixZeng could you share all the files including the PS PMMA base files you edited? |
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Yes, @fgrunewald the oplsaam.ff and the PS PMMA file as attached. |
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@WeixZeng in order to find out why links do not apply you can run
I believe you have mixed up some atomnames in the link probably the pair section. When running
Are these typos perhaps? When running
Also this one is perhaps a typo? Other than that I think the file looks good. |
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@WeixZeng can we close this issue or transfer it to the discussions section? |
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yes for sure, thank you again for your help!
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From Dr. Fabian ***@***.***> Date 05/27/2024 22:07 To ***@***.***> Cc ***@***.***>***@***.***> Subject Re: [marrink-lab/polyply_1.0] all atomic block copolymer building (Issue #355)
@WeixZeng can we close this issue or transfer it to the discussions section?
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Thank you for creating such a wonderful toolkit. Trying to build an all atomic block copolymer model for GROMACS. Thought it should be available with the '-connect' function with the gen_seq, but don't understand the syntax:
<seq_position_macro_A>,<seq_position_macro_B>-<connect_residueA>,<connect_residueB>
Would be great if you could provide some guildlines for this, one command line, let's say, for block copolymer version of PMMA and PMA like PMMA_b_PMA should be sufficient for my case.
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