[gmx-users] Re: gmx-users Digest, Vol 53, Issue 90

Li Yang liyang1980_0_0 at 163.com
Sun Sep 21 17:19:27 CEST 2008

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 stage:0-1, 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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