Hi Ran Thank you for your reply. I'm sorry that I miss the message.
>(1) 6 eigenvalues represent rotation and translation. For (very) small >molecules, these can be quite substantial, see Carlsson and Aqvist, /J. >Phys. Chem. B,/ *109* (13), 6448 -6456, 2005. By fitting you remove the >rotation and translation. You can search the literature for papers that >discuss the QH approximation as well. The motions are not really >harmonic - this is why it's an approximation. > >I've received very similar results to Carlsson and Aqvist for benzene >and palmatic acid with GMX. > >(2) The values you get depend on the sampling and the conversion of the >simulations. To improve sampling, you have to store the coordinates >frequently enough (so you get more samples). In addition, the simulation >should be long enough to give you meaningful results - and both depend >on the system which you study. Checking for convergence can be done by >repeating the calculations on different time windows, as you suggested. Sorry, I don't quite catch your mind. How to get the convergence variation of the entropy? Whether or not the time "split" method is right? eg, time points: 0, 1, 2, 3, 4, 5. and time stageļ¼0-1, 0-2, 0-3, 0-4, 0-5, right? why not 0-1, 1-2, 2-3, 3-4, 4-5. In the maillist of gmx, the latter is not wrong because of undersampling, I don't know this meaning. Could you please offer me some suggestions or refs? The method of covariance matrix & QH can estimate the up-limit of entropy, how to know the error band ? Thank you very much. >> (3) In entropy calculations, a system need to run a long time for entropy >> convergence, the time seems to be longer than the one which needed for >> energy convergence. While, for equilibrium thermodynamics simulations, how >> to justify whether or not the system has achieving a equilibrium stage, >> based on energy convergence or entropy confvergence? >> >> (4) For the example mentioned in the paper Ioan >> Andricioaei_JChemPhys2001_115_6289. I use your perl script for entropy >> calculation. But I don't reproduce the result. The needed time of entropy >> convergence is longer than the time mentioned in the paper, and so larger of >> my entropy. >> I don't know why, perphas the simulation conditions is not right. My >> simulation files are included in the attachment. Could you give some >> suggestions? >> BTW, in line 77 of your script: $w=$ev*$u*10**(-18), Does "10^-18" mean >> nm^-2?
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