Hi, I am having some seeming difficulty with the -normalize option in g_rotacf, which calculates rotational autocorrelation functions of molecules.
My system consists of 254 SPC/E water molecules. I equilibrated (3 ns, md integrator) and ran production dynamics (2 ns, md integrator) in the NVT ensemble, using Nose-Hoover temperature coupling. I chose the cubic box size such that the density of the system is set to ~1 g/cm^3. After I completed my production run, I used following command: g_rotacf -f nvt-md.trr -s nvt-md.tpr -n allatoms.ndx -P 1 -b 0 -e 10 -o finalresults/normalized_10ps.xvg where allatoms.ndx specifies all 762 atoms in triplets of atoms, with each triplet corresponding to one water molecule. The default setting for -normalize is yes, so the above command should give me the _normalized_ rotational autocorrelation function, averaged over all molecules. I do indeed get a normalized ACF, which has C(t=0)=1 by definition. (Recently (http://lists.gromacs.org/pipermail/gmx-users/2011-June/062005.html), Justin kindly pointed out to me that, per the normalize_acf() function in src/tools/autocorr.c, the normalization is such that the ACF is 1 at time t=0.) But, on the other hand, when I use the option -nonormalize, using the following command, I get a seemingly strange result: g_rotacf -f nvt-md.trr -s nvt-md.tpr -n allatoms.ndx -nonormalize -P 1 -b 0 -e 10 -o finalresults/unnormalized_10ps.xvg When I execute this command, I obtain an ACF that is 1 at time t=0. This cannot really be the correct unnormalized result, unless by some remote coincidence the unnormalized ACF happens to be 1 at time t=0. I have posted my results at http://www.andrew.cmu.edu/user/adeyoung/june12/june12.pdf . If you have time, could you please help me think where I may have gone wrong? At first, I was convinced that I mixed up the files or did something else silly. But, I've redone it, carefully naming, opening, and plotting the results, and I get the same: both the normalized and the unnormalized ACFs are 1 at time t=0, and the coordinates in the .xvg files are identical. I am sure that I am doing something wrong, but I have not found it yet. Can you please help me think what to try next? I am using Gromacs version 4.5.4. When I want to turn off normalization of the ACF, should I use "-nonormalize" (as I have done above, and as seems to be suggested by the manual), or should I use "-normalize no"? Thank you very much for your time! Andrew DeYoung Carnegie Mellon University -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
