Dear Li Yang, I forward your email to the GMX mailing list, which may be better for you since other users can contribute as well. I'll reply there - I hope you've subscribed to the list. Ran.
Li Yang wrote: > Dear Ran Friedman > > I'm sorry to disturb you, my name is Li Yang, I'm a chinese student. > > I've read some paper about the calculation of QH entropy: > (a)Jurgen Schlitter_ChemPhysLett1993_215_617, > (b)Ioan Andricioaei_JChemPhys2001_115_6289(quasiharmonic approximation). > There is still something confuse me. > > (1) Why the number of the eigenvalues is 3n-6 (the last 6 values are close to > zero) but not 3n ? I practice some small examples by gromacs. (256 argon > atoms in a box of 2.3nm^3, you can find this example in paper(b)). For > g_covar, when -nofit, the number of eigenvalues is 3n; when -fit the number > is 3n-6. It seems there are some freedoms constrainted in the "fit" process. > > The paper' conclusion is based on a assumption that hw<<kT, say, the high > frequencies vibrate (both rotation and translations, right?) can be omitted > for the entropy calculations, as it were, the contributions of them is too > small to be omitted. Are the freedoms mentioned above represent the freedoms > of rotations and translations of the molecules. I don't know. Maybe the > answer is in those papers, but I cannot catch it. > > While how to use the "nofit" result and "fit" result? The eigenv.agr in the > attachment includes "fit" and "nofit" results for the example: 256 argon > atoms in a box of 2.3nm^3. Why there is a big difference between them? > > > (2) I "split" some time-segment to obtain the entropies in each stage to get > the convergence variation of the entropy. But I doubt the feasibility of this > method. If wrong, how to do? > 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? > > > (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? > > I apologize in advance if I disturb you. > Thank you very much. Waiting for you reply. > > > Best > > Li Yang > > > Li Yang > [EMAIL PROTECTED] > 2008-09-17 > -- ------------------------------------------------------ Ran Friedman Postdoctoral Fellow Computational Structural Biology Group (A. Caflisch) Department of Biochemistry University of Zurich Winterthurerstrasse 190 CH-8057 Zurich, Switzerland Tel. +41-44-6355593 Email: [EMAIL PROTECTED] Skype: ran.friedman ------------------------------------------------------ _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
