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normal simulation parameters

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11 years 3 months ago #1365 by Tooba
simulation parameters was created by Tooba
Hi dears
I'm a new applier of martinize to generating CG form of my own dendrimer.First of all I want to ask you is this script suitable for any kind of polymers like PAMAM or this will need to change some parameters. consider that it just need to have .pdb form of our FG structure.

Best regards

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11 years 3 months ago #1368 by djurre
Replied by djurre on topic simulation parameters
martinize.py is only meant to generate protein structures/topologies. However, for a 5th generation PAMAM polymer, a topology is available on this website (Downloads > Force field parameters > martini_v2.0_polymers.itp). A gro file you would have to generate yourself, but using thorough energy minimization and slow relaxation you generate one from a random structure (eg. a box of water).

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11 years 3 months ago #1369 by Tooba
Replied by Tooba on topic simulation parameters
Thanks for your response

About G5 of PAMAM,yes I had seen befor, but i didn't know this martinize is used for proteins only. So it's not suitable to apply for other dendrimers(polymers). For this purpose we should write another script of our own?!

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11 years 3 months ago #1372 by djurre
Replied by djurre on topic simulation parameters
yes.

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