[gmx-users] Build polymers with pdb2gmx

[Li, Shi]

Dear GMX users,

I am new to polymer simulation and want to build a polymer system for
Gromacs. I have followed Justin's instruction to make polyethylene by
editing the rtp and hdb file. But I have a couple of questions regarding a
larger polymer configuration:

1. The example system (polyethylene) only has one repeat unit, is there a
way to define the number of repeat unit and then generate the PDB file? I
am also wondering if there is a way to make the configuration with random
torsion? I currently use Gaussview to copy and paste, and the initial PDB
is just a linear chain. Like this...^^O^^O^^O^^
2. Since the PDB file is straightly from Gaussview, the atom names in the
file are all in basic form (C, H, O...), in order for the pdb2gmx to work,
I have to manually match and replace them according to the .rtp file. For
larger repeat unit, is there a better way to do this?

Thanks for your help and suggestions.

-- 

Shi Li

Research Assistant, Ph.D. Candidate
Department of Chemistry &
Center for Applied Energy Research (CAER)
University of Kentucky

Email: sli259 at g.uky.edu