Hi Clemens, As Charles pointed out in his note on 7/25,
> The script doesn't appear to be particularly robust as it seems to > blow > up during dynamics unless I reduce the time stepsize to 0.001 ps. > Use of > the variable stepsize feature of the IVM would probably fix this, > though. The ATMCHK error you're seeing is caused by a solvent atom moving too far from the center of the coordinate system, so that its position has a coordinate greater than 9999 A. I glanced through the scripts, and the only energy term holding the waters in place that I noticed is the electric field. Thus, if a particular water molecule gets going fast enough, there'll be nothing to keep it bound near the protein. It'll go flying off into space, eventually triggering the ATMCHK error. Individual atoms can get heated up quite a lot by integration errors during molecular dynamics. If, for example, two atoms move from being close, but not overlapping, to overlapping each other significantly in the course of one dynamics step, then the system has instantaneously gained a whole bunch of potential energy. Those two atoms in our example will spring away from each other, having heated up significantly. So how can you avoid this kind of behavior? You have two choices: 1. Change the timestep settings in Jens's h20refinenew2.xplor (just search through for 'time'). He has them all set at 5 fs, which is rather agressive for Cartesian-space dynamics. Dropping them all to 1 or 2 fs should eliminate the problem, as Charles pointed out. But remember to increase the number of dynamics steps in each case to keep the total time constant. This will, unfortunately, increase the CPU time per structure. 2. Switch the scripts from using the Langevin dynamics engine to using Charles's internal variable dynamics engine. Turn on its variable-stepsize setting. This will cause the dynamics engine to take short timesteps in situations where large steps could inject a lot of energy into the system (as per our example above), but allow the dynamics integrator to take long timesteps in areas where it can get away with it. This should eliminate the ATMCHK error without costing too much CPU time. Hope this helps. --JK On Aug 14, 2007, at 10:16 PM, Clemens C. Heikaus wrote: > Hello, > > I have a very similar problem like Martin. I tried to run water > refinement with XPLOR-NIH 2.16.0 and used the example files from > ftp://ftp.pasteur.fr/pub/BIS/linge/ to see whether it is running > correctly but get the following error message after approx. 2 > minutes in which it runs just fine. For my real case (155 residues > plus organic non-bound ligand) I have tried water refinement with > the recoord shell scripts and it was the same error message. > > %ATMCHK-ERR: unknown coordinates for atom "WAT1-386 -TIP3-H1 " > %ATMCHK-ERR: Unknown coordinates > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > BOMLEV= 0 reached. Program execution will be terminated. > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > Subroutine DIE called . Terminating > > Do you have any ideas what the problem might be? Help would be very > much appreciated. > Clemens > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://dcb.cit.nih.gov/pipermail/xplor-nih/attachments/20070814/8f9fd2df/attachment.html
