On Sat, Nov 9, 2013 at 9:36 AM, alex.bjorling alex.bjorl...@gmail.comwrote:
Dear users,
I am investigating protein crystal packing artifacts by doing equilibrium
simulations starting from a crystal structure. I would like to know if the
relaxations i see are reproducible, in the sense that many simulations with
independent velocities give the same general result.
My plans is to do only one set of (first NVT then NPT) equilibrations with
position restraints. Then, I thought I'd do a shorter NPT run with position
restraints, with more frequent output and using the trr snapshots as
starting points for production runs.
The only question then is how far apart these snapshots need to be to
guarantee independent velocities. Attached is the velocity autocorrelation
for the Protein group. It seems to me that using snapshots 1ps apart would
do it, since the autocorrelation has decayed by then.
Is this a valid approach?
That the observations are uncorrelated (because the autocorrelation time
has elapsed) does not imply that trajectories started from successive
snapshots would be independent - in the absence of floating-point or
load-balancing artefacts leading to numerical divergence, the separate
simulations would nearly reproduce each other! Since you have to wait for a
period of divergence anyway, you might as well generate new velocities
after an initial stage of equilibration, equilibrate further, and have no
independence question to answer.
Mark
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