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From: Gkourmpis, Thomas (Thomas.Gkourmpis_at_borealisgroup.com)
Date: Thu Apr 26 2012 - 03:51:45 CDT
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Hello everyone
I've just started using VMD and I have a question regarding how to build a polymer for subsequent molecular dynamics runs.
I can build (or obtain) monomer units in pdb format but how can I tell the computer to put them in a specific sequence in a random manner as to create an actual coiled chain?
For example I want to build a polyethylene chain and I need two CH3 units (chain ends) and a CH2 unit (monomer). I need a way to put the CH3 units in the end and the CH2 units connected with the torsion rotations in a random manner.
Thank you very much in advance
Thomas
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