Widya Desmarani wrote:
Dear gromacs user,
I have been trying to look for an answer for my following question from
our forum but still couldn't manage to find one. Probably it is trivial
but I am not sure.
Instead of running a single relatively long simulation (say for about 30
ns), is it acceptable if we simulate multiple short simulations (say 15
simulations where each of them is 2 ns), and then, all the resulted
trajectories are merged/concatenated into one single trajectory with the
amount of total simulation 30 ns? I am interested in investigating bulk
properties of liquid, such as compressibility, diffusion, and dielectric.
There is no need to concatenate the trajectories, and moreover it may give you a
misleading result. Every simulation needs time to equilibrate. In the limit of
infinite sampling, all simulations should converge to the same properties, on
average. Whether or not your simulation can produce stable properties in 2 ns
is something you'll have to decide. If 2 ns is insufficient, then you're still
not collecting data that are as reliable as you would get from a longer
simulation.
Multiple simulations from independent starting velocities and/or configurations
are generally expected. A single simulation does not necessarily tell you the
whole truth.
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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