[gmx-users] Large branched and crosslinked polymer

Luke Pestl luke.pestl at utoronto.ca
Thu Feb 8 15:50:47 CET 2007

I am new to gromacs and I am trying to model a system that has a protein 
and a fairly large and complex random polymer.  I am having trouble 
adding the polymer to the system.  PRODRG was useful with a small 
segment of the polymer, but I would like to use a much larger molecule.  
I thought I could enter the monomers into the rtp file, but because it 
is randomly branched and cross linked I do not know if this is 
possible.  The description of x2top sounded hopefull, and I thought that 
it might be able to generate an rtp entry for me, but I cannot get the 
program to work because I cannot find the n2t library files that it 
requires (am I supposed to make these files, or should they have been in 
the package somewhere?). 

Any suggestions as to how I should proceed would be greatly appreciated.

Luke Pestl

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