[gmx-users] Replicating an experiment

[David van der Spoel]

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.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se