normal beta carotene configuration file

  • esra
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1 year 3 months ago #7536 by esra
beta carotene configuration file was created by esra
Hello Users,

I'm planning to use coarse grained beta carotene in my simulations. I have found the topology file form the website, thank you. But I also need a coarse grained configuration file (a .gro or a .pdb). How can I find or form it?

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1 year 3 months ago #7537 by peterkroon
Replied by peterkroon on topic beta carotene configuration file
Hi Esra,

you can make one by taking an atomistic conformation, and make a CG one by putting the beads on the center of masses of the constructing atoms.
Alternatively, put beads more or less in the right place (for example, randomly in space), and do a vacuum minimization and (short) equilibration.

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1 year 3 months ago #7538 by Pim
Replied by Pim on topic beta carotene configuration file
Peter's right, in general any atoms in roughly the right coordinates will work if you do a short energy minimization. Luckily for you, you can also copy this:

BCR
10
1BCR R1 1 3.647 3.525 3.474
1BCR R2 2 3.456 3.630 3.637
1BCR R3 3 3.671 3.795 3.584
1BCR T1 4 4.060 3.875 3.468
1BCR T2 5 4.414 3.685 3.160
1BCR T3 6 4.880 3.482 3.008
1BCR T4 7 5.299 3.352 2.762
1BCR R4 8 5.614 3.155 2.596
1BCR R5 9 5.821 3.189 2.417
1BCR R6 10 5.747 3.412 2.555

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1 year 3 months ago #7540 by esra
Replied by esra on topic beta carotene configuration file
Many thanks to both of you!

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