On 2010-12-25 15.05, NG HUI WEN wrote:
Dear all,
Merry Xmas! I have a very quick question here which i'd like to pick
your brain on, would really appreciate a reply.
I am planning to replicate an experiment that I have carried out. Just
wondering what is the best way to do it? I am thinking of changing the
starting velocity of my system by setting a random number e.g 23412445
etc in the gen_seed section as below, not sure if it is meaningful to do so?
gen_vel = yes
gen_temp = 300.0
gen_seed = random number
Thank you for your input!
That will work fine, if you simulate long enough. Consider that the
starting structure may also influence how different your results will
be, e.g. for a protein in water. For liquids there is no such problem.
You can do a simulation and slightly elevated temperature and pick
structures from that with a different random seed, in order to randomize
your simulations even more.
HW
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David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
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