Hi all, I am running a series of umbrella sampling simulations of a drug across a membrane, with the final aim to determine permeability using the local diffusion model.
I have come across papers where the (necessary) autocorrelation times of the mean-squared fluctuation of the coordinates are calculated using gmx wham, and this is also what I have done like this: gmx wham -if pullf-files.dat -it tpr-files.dat -o -hist -ac -oiact and then the ac-times are written to the file iact.xvg. To understand better the procedure however, I also wanted to do a similar calculation manually. I therefore did this: gmx traj -f ../umbrella0.part0001.xtc -s ../umbrella0.tpr -ox umbrella0_z_com.xvg -com -nox -noy to extract the z-com-coordinates of the drug molecule for a particular us window. Then: gmx analyze -f umbrella0_z_com.xvg -ac -fitfn exp Followed by: gmx analyze -f autocorr.xvg -integrate to get what I though was going to be the equivalent acf-time tau. However, for this umbrella window gmx wham gives me tau = 2.25 whereas the second approach gives a value of 122. What could be the reason for this difference? There is some info in cmx wham that says that the act calculation is cut at a value of 0.05, and that is something that I haven't been able to replicate in my second approach, but any insights are highly appreciated. Cheers /PK -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
