From: Sachin Natesh (snatesh_at_uchicago.edu)
Date: Thu Sep 10 2015 - 19:13:41 CDT
In the NAMD controller class reference, which can be found here
notice a possible error in the computation of the adaptive tempering
temperature update (lines 1875-1878; see below)
01875 //dT is new temperature
<http://www.ks.uiuc.edu/Research/namd/doxygen/common_8h.html#a40> dT =
01877 dT += random
01878 dT += adaptTempT;
On line 1877, the stochastic portion of the temperature update is added to
what has been computed for the new temperature thus far, though the
integration time-step, adaptTempDt, is placed within the sqrt function.
This seems particularly erroneous to me as *equation 1* of the paper upon
which the NAMD implementation is based (here
<http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2905458/>) calls for the
integration time-step to fall outside of the radical, which can be realized
through simple cross multiplication of the dt differential.
Does the NAMD implementation of the adaptive tempering algorithm actually
contain this error, is it the online documentation that is flawed, or am I
Any information in this regard would be much appreciated.
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