Date: Fri, 11 Nov 2016 15:28:26 +0100
Dear AMBERs,
I'm calibrating some GIST calculations. In particular, I'm checking how
a number of frames (equidistantly distributed through the equilibrated
simulation) taken for GIST calculations affects the values of GIST
energy components. The reason to do this is to find an optimal length of
my simulations (and a number of frames to analyze with GIST) for a
system I study so that the values I obtain are converged. I found a
common feature independently of regions, sizes a box used for GIST and
lengths of the simulations within the ranges I'm working in. So E(sw),
E(ww) and TS(orientational) converge very similarly: the values go down
monotonically with the increase of number of frames taken into account
for the calculations and converge for several thousand of frames (exact
number depends on the system and simulation type). This result is
something one can expect. However, TS(translational) behaves essentially
differently: its value drops when increasing the number of analyzed
frames to ~200 and then it goes up again (one of the examples is
attached for 10000 frames from 100 ns long simulation). What could be
the reason for such a non-monotonic behaviour? Is the decrease observed
simply due to an artifact of the calculations when the number of frames
too low?
Thank you very much and cheers,
Sergey
-- Sergey A. Samsonov Postdoctoral researcher Structural Bioinformatics Biotechnology Center Tatzberg 47-51 01307 Dresden, Germany Tel: (+49) 351 463 400 83 Fax: (+49) 351 463 402 87 E-mail: sergey.samsonov.biotec.tu-dresden.de Webpage: www.biotec.tu-dresden.de
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(image/png attachment: TS_translational_example.png)
