[gmx-users] model polymers

[Jason DeJoannis]

That is coming from the lincs initialization, where a constraint
neighbor-list is constructed. The B topology is usually not used
unless you are doing a special free energy simulation. The message
means that either both shakeA & shakeB have to be zero, or they both
have to be non-zero. Do you have constraints? You can send me your files,
but I can't promise anything ;)  Note also that "mdrun -debug" will
print more data.

---
Jason de Joannis, Ph.D.
Chemistry Department, Emory University
1515 Pierce Dr. NE, Atlanta, GA 30322
Phone: (404) 712-2983
Email: jdejoan at emory.edu
http://userwww.service.emory.edu/~jdejoan



> From: "Marcelo A. Carignano" <cari at purdue.edu>
> To: gmx-users at gromacs.org
> Date: Tue, 04 May 2004 09:36:57 -0500
> Subject: [gmx-users] model polymers
> Reply-To: gmx-users at gromacs.org
>
> 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
>