From: Jun Zhang (coolrainbow_at_yahoo.cn)
Date: Wed Oct 26 2011 - 19:00:18 CDT
Dear Mert :
Actually this is not strange. If your simulation time is not long enough then the sampling errors will give the heat capacities a large deviation.
Also, is the simulation compatible with the experimental condition? Ensemble, cutoff values, pH or protonation states of protein?
Moreover, in my opinion, the thermodynamics measurements of such macromolecules seem to be inherently low precision and the experiment data should be
carefully checked.
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Jun Zhang (coolrainbow_at_yahoo.cn)
Computational Chemistry Group
No.94, Weijinlu
Nankai University
Tianjin, China
________________________________
发件人： Mert Gür <gurmert_at_gmail.com>
收件人： NAMD list <namd-l_at_ks.uiuc.edu>
发送日期： 2011年10月27日, 星期四, 上午 2:44
主题: namd-l: Evaluated heat capacities via NAMD are larger than experimental values
Dear all,
I evaluated the heat capacities of some proteins as given in the NAMD
tutorial. I obtained the internal energies via NAMDenergy. However,
the heat capacities I get are up to 4 times as large as experimental
ones.
It would be great if someone could tell me the reasoning behind this
or refer to a publication.
Best,
Mert
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