[gmx-users] model polymers

Marcelo A. Carignano cari at purdue.edu
Tue May 4 16:38:00 CEST 2004

Gromacs users,

	I am new to Gromacs and I am trying to create a minimal
force field to simulate 1 (one) model polymer chain (for now).
I want this polymer to be a string of 20 beads, connected with Morse
potential. After reading and trying several options, I think I am
very close to succeed, but not there yet.

This are the steps I have followed:

1) Create a PDB file with my chain: chain20.pdb

2) Create a new collection of force field files: ffpoly*.*

   Theses files are:

   ffpoly.rtp, ffpoly.atp, ffpoly.hdb, ffpoly-n.tdb, ffpoly-c.tdb

3) Run: pdb2gmx -f chain20.pdb -ff poly

4) Run: editconf -box 10. 10. 10.

5) Get some more ffpoly*.* files:

   ffpoly.itp, ffpolynb.itp, ffpolybon.itp

6) Get grompp.mdp (from the water216 example)

7) grompp -maxwarn 1000

8) mdrun

     FAIL with this message:

     Fatal error: It is not allowed to have a constraint length zero and
non-zero in the A and B topology


I understand that without all the files very little can be said.
Even if they are short files, it may be kind of messy to list them here.
If anyone is interested in the problem and/or wants help me
with that I can e-mail a tar file with all the information.

Waiting for your answers, 

	Marcelo Carignano
	cari at purdue.edu

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