[gmx-users] construction of homopolymer from non-standard monomers in gromacs

Justin A. Lemkul jalemkul at vt.edu
Wed Mar 28 17:46:02 CEST 2012

Иимяа Фаамиилиияа wrote:
> Hi,
> I am trying construct  homopolymer from non-standard  monomers .
> I have pdb, itp and gro files for monomer and constructed pdb file for polymer. 
> I can put them in corresponding  top/forcefield.ff directory.
> But how I can get itp and gro files for polymer (for example, for 3-mer in simplest case)?
> How Gromacs knows which atoms are "head" and "tail" atoms for connection of monomers 
> into polymer (like in "Material Studio")?

The best approach is to build .rtp entries and have pdb2gmx build your topology 
for you.  That way, you can build polymers of any size you like.  See the 
instructions and linked example at:




Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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