Hi, The easiest way to fix the problem is to decrease the current timestep. Also please read about -dd and -rdd keys of mdrun utility.
Vitaly > One of my simulations just crashed after 660,000 steps with the > following message: > > Step 660560: > The charge group starting at atom 4100 moved than the distance allowed > by the domain decomposition (1.500000) in direction X > distance out of cell 2.356293 > Old coordinates: 1.752 0.447 0.751 > New coordinates: 3.593 1.532 0.674 > Old cell boundaries in direction X: 0.000 2.116 > New cell boundaries in direction X: 0.000 2.122 > > ------------------------------------------------------- > Program mdrun, VERSION 4.0.5 > Source code file: domdec.c, line: 3651 > > Fatal error: > A charge group moved too far between two domain decomposition steps > This usually means that your system is not well equilibrated > ------------------------------------------------------- > > "Why Weren't You at My Funeral ?" (G. Groenhof) > > Error on node 0, will try to stop all the nodes > Halting parallel program mdrun on CPU 0 out of 8 > > I am modelling flexible alkyl chains which are anchored to a frozen > silica wall. This particular atom (4100) is at the edge of the > periodic boundary condition so I am guessing that what happens is that > while the anchored side stays where it is, the other free end wanders > into the next cell and this perhaps triggers the error message? If > this is indeed the problem, is there some way to stop the program > stopping with an error message when this happens? > > I did do an energy minimisation before starting and my structure looks > OK. It seems strange that it would crash only after 660000 steps. > > Also what is meant by the following? I am using NVT so my simulation > cell should not change. > > Old cell boundaries in direction X: 0.000 2.116 > New cell boundaries in direction X: 0.000 2.122 > > > My cell is about 4.3 x 4.3 x 7.5 nm > I am using gromacs-4.0.5 > > Thanks -- gmx-users mailing list [email protected] http://lists.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
