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.
alpay Date: Sat, 25 Feb 2006 16:57:42 +1100 (EST) From: "Mark Abraham" <[EMAIL PROTECTED]> Subject: Re: [gmx-users] lincs contraint failure To: "Discussion list for GROMACS users" <gmx-users@gromacs.org> Message-ID: <[EMAIL PROTECTED]> Content-Type: text/plain;charset=iso-8859-1 > Dear all > > i am trying to simulate a zinc-finger peptide using explicit solvent and g43a1 > forcefield and backbone constraints . I have managed to simulate using coulomb cut off for electrostatics. But i would also like to simulate using > 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? Mark -- --------------------------------------------------- N. Alpay Temiz | Department of Computational Biology & | Department of Molecular Genetics and Biochemistry | School of Medicine, University of Pittsburgh | e-mail:[EMAIL PROTECTED] | --------------------------------------------------- _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
