[gmx-users] model polymers
jdejoan at emory.edu
Thu May 6 16:12:23 CEST 2004
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
> 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
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