VMD-L Mailing List

From: Gkourmpis, Thomas (Thomas.Gkourmpis_at_borealisgroup.com)
Date: Thu Apr 26 2012 - 03:51:45 CDT

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 This Email and any files transmitted with it are confidential and intended solely for the use of the individual or the entity to whom it is addressed. If you have received this Email by error, please notify the sender and delete the material from any storage device. Borealis extends no warranties and makes no representations as to the accuracy or completeness of the information provided. It is the customer's responsibility to inspect and test our products and technical advice in order to satisfy itself as to the suitability of the products and technical advice for the customer's particular purpose.