Hi Franz, This is a fairly common problem using the 'classic' xplor dynamics engine. It can be caused by several things:
1. Bad covalent restraints (bonds, angles, etc), caused by bad parameter sets. If you're using the current protein.par and protein.top files, that's probably not the issue. 2. Bad distance restraints (and to a much lesser extent, bad covalent restraints). In this context, 'bad' could mean too tight a distance range, too high a force constant, or inconsistent with each other. 3. Bad luck. Try running with a different random number seed. Of these, the most common problem is distance restraints that are too tight or inconsistent with each other. Particularly if your temperature explosions are occurring at the beginning of the cooling phase, because that's when full vdW restraints are added in, and so some distance restraints that could be satisfied by coordinates that included vdW overlap suddenly start fighting with the vdW term. N.B. If you're using Charles's internal variable dynamics engine, you can set it to avoid this problem a lot of the time by allowing it to take variable-sized timesteps. That prevents the simulation from injecting extra energy into the system in regions where the potential energy surface is changing steeply. Hope this helps. JK On Nov 27, 2007, at 1:48 PM, Franz Hagn wrote: > Hi all, > > during the xplor calculation (with sa.inp script and xplor 2.16), > after > high temperature dynamics, I get unusual high temperature and abortion > of the run. Does anybody know some hints? Are my restraints to > rigorous ? > Thanks, Franz > _______________________________________________ > Xplor-nih mailing list > Xplor-nih at nmr.cit.nih.gov > http://dcb.cit.nih.gov/mailman/listinfo/xplor-nih
