[gmx-users] lincs contraint failure

Nuri A Temiz temiz+ at pitt.edu
Mon Feb 27 17:04:16 CET 2006

Dear Mark

The mdp file is how it should be. I also did a cut-off run from the same 
starting point and it runs. 
For the PME i have tried to decrase the time step to 1 fs. that did not work
either. The protein is exploding and simulations is crashing. 


Date: Sat, 25 Feb 2006 16:57:42 +1100 (EST)
From: "Mark Abraham" <mark.abraham at anu.edu.au>
Subject: Re: [gmx-users] lincs contraint failure
To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
Message-ID: <12234. at sqmail.anu.edu.au>
Content-Type: text/plain;charset=iso-8859-1

> Dear all
> i am trying to simulate a zinc-finger peptide using explicit solvent and
> forcefield and backbone constraints . I have  managed to simulate using
coulomb cut off for electrostatics. But i would also like to simulate
> PME. when i run the simulation at step 0 it gives constraint failure and
stops. i am at a loss.
> I am attaching the mdp file and the log file
> I would very much appreciate any help

I can't see anything obviously wrong with the .mdp file. Check using diff
that the differences between it and whatever you modified it from are what
you expect. Answering the following questions might illuminate the
situation - What is your starting point? Are you using the configuration
you intend to use? Can you do a cut-off simulation from that point?


N. Alpay Temiz					  |
Department of Computational Biology &		  |
Department of Molecular Genetics and Biochemistry |
School of Medicine, University of Pittsburgh	  |
e-mail:temiz at pitt.edu				  |

More information about the gromacs.org_gmx-users mailing list