Hi, I have run a simulation of 254 SPC/E water molecules in a cubic box of edge length 19.660 Angstrom. I have used the gromacs utility g_velacc to calculate the velocity autocorrelation function for the motion of only the oxygen atoms. When I plot the velocity autocorrelation function versus time, my result is a curve with more than one local minimum.
My question is, should I expect having more than one local minimum? I am not sure that my result is reasonable. For example, the Democritus molecular dynamics website gives one example of a velocity autocorrelation function, although they do not specifically say what system (water or something else?) or what state (liquid or gas?) was used: http://www.cse.scitech.ac.uk/ccg/software/Democritus/Theory/vaf.html . Their plot shows one "strong" local minimum and one "weaker" one; both of these local minima are in the negative regime. I am new to this field, but I believe that the "strong" local minimum corresponds conceptually to the recoil of the atoms when they collide. If you have time, could you please look at my result at http://www.andrew.cmu.edu/user/adeyoung/velacc_may23.pdf and see if you think it is a qualitatively reasonable result? My main concern is the first local minimum, which I have labeled with an arrow on the plot. This minimum is in the _positive_ regime, which I believe (but I am not sure) cannot correspond to the recoil of atoms when they collide. In my pdf file I have displayed the parameters I have used for equilibration and dynamics. To summarize, I have used the leap frog algorithm with 2 ns equilibration in 1 fs steps, and 5 ns dynamics in 1 fs steps. For dynamics, I have saved configurations every 2 fs. Although my result from g_velacc has velocity autocorrelation frunction data from 0 to 1000 ps, the function decays rapidly to zero (as it should, I think, because the velocity rapidly decorrelates since the atoms/molecules "forget" their initial velocities), so I have plotted only from 0 to 1 ps. I am running Gromacs version 4.5.4. Thank you very much for your time. Andrew DeYoung Carnegie Mellon University -- gmx-users mailing list gmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists