Hi Bob and others,
> Regarding changing the seed in langevin dynamics runs - this is very
> important. One should absolutely be careful to do this to get valid
> results, and this is not yet automated in pmemd (next release). Please
> see
> Cerutti, Duke, et al, J Chem Theor Comp 4, 1669-80 (2008).
This reminds me of something we should probably discuss at the AMBER
developers meeting. I propose that we change the way ig works and we should
try to make sure this gets put into both sander and pmemd. My proposal is
that +ve values of ig should behave as they do now. Then if one sets a value
of ig=0 then it uses the time of day in microseconds for the random number
stream. If however, one sets a -ve value for ig then it uses the absolute
value of that as the seed BUT it does not attempt to synchronize the random
numbers in any way between processor threads - removing the parallel
bottleneck problems with langevin for example. Thus in this case (excluding
load rebalancing etc) one should get the same results (for a few steps)
providing the same number of processors are used. Obviously it is more
complicated than this but I don't think we should worry about that.
Clearly on 1cpu -ig = ig.
In the case of ig=0 we would need to decide whether or not random numbers
are synchronized between threads but I vote not to do this since for
Langevin as far as I can tell the current approach of enforcing the
synchronization of random numbers is crazy and doesn't help with the actual
accuracy at all - in fact it allows people to introduce very weird
correlations.
Thus +ve ig values would essentially be reserved for testing and all actual
production runs would / should be run with ig=0 (which is actually -1 right
now in amber 10 - hence why there would be changes). The key then becomes
whether we change the default value of not - which I also think we should
do. And then we explicitly set if in all the test cases so they are still
usable...
What do you think?
All the best
Ross
/\
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|\oss Walker
| Assistant Research Professor |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
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Received on Fri Dec 19 2008 - 01:10:27 PST
