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---- Jeffrey I pasted here one of the relating posts by Bob. --------- Germain - ig is used for computing random velocities during a restart that does NOT have velocity information (eg., from a minimization), and for the andersen and langevin thermostats (ntt 2, 3 respectively). You can get artifactual behaviour in the thermostats if you use the same seed in restarts, as you need to be effectively sampling from a gaussian distribution over the entire run, not resampling from the same sequence of pseudorandom numbers repeatedly. So in using these thermostats it is important to be careful about changing the value of ig through your restarts, or strange things can happen. There is a facility in sander to use the system clock to get the random seed, probably only in amber 10 (sorry, I don't have amber 10 doc available at the moment), and don't see it described in 9). I don't have this capability in pmemd yet. The best way to do this stuff is to carry the state of the rng forward between restarts; I plan to do that in pmemd in the future. Regards - Bob Duke __________________________________________________ ¸Ï¿ì×¢²áÑÅ»¢³¬´óÈÝÁ¿Ãâ·ÑÓÊÏä? http://cn.mail.yahoo.com _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amberReceived on Fri Feb 20 2009 - 01:08:00 PST