normal Aggregation of Polymers

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11 years 3 months ago #1293 by xudongh
Aggregation of Polymers was created by xudongh
Hello all,

I would like to investigate aggregation behaviors using CG models, I have written a .gro and topology file for 1 of such polymer and defined bonding orders in my itp file. However, I wish to inviestgate the aggregation of many of such identical molecules, (which involves like 20 of those molecules, and it increases the total amount of atoms from 100 to 1000 roughly), do I have to write/define bond orders of each bead all the way to the 1000 range because of this? OR is there an easy way to auto produce multiple molecules in a system to investigate the aggregation process?

Please let me know, thank you.

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11 years 3 months ago #1294 by djurre
Replied by djurre on topic Aggregation of Polymers
This is more of a Gromacs question ( www.gromacs.org ).

Assuming you have several of the same molecules, you only need to specify bonds/angles/etc for one molecule. On the bottom of your .top file you set the number of molecules in your system, eg (assuming 10 polymer molecules with molecule name POL and 100 water beads):
10 POL
100 W

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11 years 3 months ago #1295 by xudongh
Replied by xudongh on topic Aggregation of Polymers
@ Djurre,

Thank you for the suggestion and kindly response. I tried searching gromacs manual for such problem but I couldn't really identify a working solution. However, prior to asking, I tried exactly what you suggested, but it gave 2 problems. 1st one is if I change the polymer number in the topology file and do my usual run, it states number of molecules in .gro is inconsistent with what is defined in topology, because defining i.e 10 for POL would mean 10x of however many atom in .gro. Second, I somehow got it to work by manipulating the atom numbers to match the .gro, but the result (viewed in VMD) shows the extra molecules are in loose bonding with each other, not in the structure bonding order I specified originally within the .itp for the 1st molecule.

I know this is kind of out of bound question for this site, please let me know if this is too much to work with, and I will attempt to post this in the gromacs mail list.

Thanks @ Djurre.

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