AMBER Archive (2009)

Subject: [AMBER] IG not change at each restart of NPT simulation

From: Jeffrey (jeffry20072008_at_yahoo.cn)
Date: Wed Feb 18 2009 - 06:49:47 CST


Dear all,

   I read previous posts discussing ntt=3 or 1 for NPT simulation. I performed a 30-ns npt trajectory using ntt=3 and ig=default at each restart (1.6 ns per segment) to monitor the conformational dynamics of a protein system. But some posts have mentioned that IG should change its value at each restart otherwise artiactual behavior can be observed. I'd like to know more in detail about how ig=default at each restart will effect my observation when I only concern on the conformational dynamics? Should I rerun the simulation from just the starting model?

Many thanks.

----
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

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