Hi Blaise, You'd better look in the log file where this starts. I bet it's either Lys-NH3+ or phosphate (ATP?) spinning like crazy. Check the archive for solutions.
Best, Tsjerk On 10/2/07, Blaise Mathias-Costa <[EMAIL PROTECTED]> wrote: > > Hi all, > > The mdrun stopped after 2.6nS after writing this error: > Step 1321571, time 2643.14 (ps) LINCS WARNING > relative constraint deviation after LINCS: > max 2.814066 (between atoms 2742 and 2745) rms 0.041434 > bonds that rotated more than 30 degrees: > atom 1 atom 2 angle previous, current, constraint length > 2742 2743 90.1 0.1728 0.0946 0.1000 > 2742 2744 90.0 0.1010 0.2410 0.1000 > 2742 2745 90.0 0.1675 0.3814 0.1000 > > like this for 100s of times.. > > here is the md.mdp file: > cpp = cpp > include = -I../top > define = > integrator = md > dt = 0.002 > comm_grps = Protein > nstcomm = 1 > nsteps = 2500000 > nstxout = 5000 > nstvout = 5000 > nstlog = 5000 > nstenergy = 500 > nstxtcout = 250 > xtc_grps = Protein > energygrps = Protein non-protein > nstlist = 10 > > > Blaise Mathias Costa, PhD > Department of Pharmacology and Experimental Neuroscience > University of Nebraska Medical Center > Omaha, NE 68198-5800, USA. > Tel: 001 402 559 7132 > > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > 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 > -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623
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