Re: Evaluated heat capacities via NAMD are larger than experimental values

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. ---------------------------------------------------------------- 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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