Hi all,
I hope that the details of steered MD method employed in AMBER be explained
more for non-professional users through the manual. During a pulling
simulation, such as DNA pulling, a force-extension curve can be obtained
from the output file which is generated by setting jar=1 (i.e. k*(x-x0) vs.
x). I’m not sure that if this curve can be compared with a similar curve
which is obtained from an experimental simulation (assuming the time scale
in the two cases are nearly equal); or firstly the potential of mean force
must be calculated and then forces obtained as derivative of the PMF?
Any comments would be greatly appreciated.
Thanks in advance
--
Ali
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Received on Tue Apr 12 2011 - 10:30:06 PDT
