Hi, perhaps this problem is related to bug 774:
http://redmine.gromacs.org/issues/774 which has been discussed quite often, recently. Somehow there is a problem in the order of removing the PBC and jumps. As already mentioned, I could solve the problem by providing a trajectory with whole molecules to g_msd. An indexfile with seperate groups for every molecule has to be created and finally every single molecule group has to be analyzed, but WITHOUT the -mol flag. Afterwards the resulting MSDs only need to be averaged. /Flo On Mon, 2012-03-19 at 14:31 +0200, Ioannis Beis wrote: > Dear Gromacs users, > > I have been trying to calculate the lateral MSD of lipid molecules > within a bilayer. I have performed simulations in a rectangular box > with PBC. I have used trjconv with -pbc nojump. I compared results > between the initial trajectory and the one generated by trjconv for 6 > different lipids. In 5 cases the calculated MSD was identical and only > in one there was difference (big difference). According to the > results, MSD loses linearity and exhibits large fluctuations after > some point. The above give rise to the following concern. > > As far as I understand, -pbc nojump checks if any molecule crosses the > box boundaries and if yes it brings back the broken part from the > symmetric side to the original place, keeping the molecule whole. This > way box information is lost, but each molecule is supposed to have > continuous trajectories. The true continuity of trajectories, however, > is only secured only if .xtc files carry all information of boundary > crosses based on the time step of the initial run in addition to all > coordinates for all times. Otherwise, the result is clearly dependent > on the frequency of saving and continuity is not guaranteed. > > E.g. in my case -I have small frequency of saving (100 ps) for long > simulations to avoid very large output files- one can't tell based > merely on the coordinates whether or not a lipid crossed boundaries > between two consecutive frames. Of course if the lipid went back and > forth then the result of the calculation would not be affected but > only by statistical means; however if the lipid had an overall > translation across the box (not captured by -pbc nojump because the > molecule is whole in both frames), then the calculation is destroyed. > > If this is the case, it seems to me that g_msd might in practice give > correct results for proteins, but for smaller molecules the > reliability of the results depends sensitively on molecule > size-frequency of saving coordinates relationship and might give rise > to huge systematic errors. > > Is there a way to obtain a converted trajectory that guarantees > unconditional continuity, so that one makes sure that he obtains the > proper MSD for his molecules? > > Thank you in advance! > > Best regards, > Ioannis > > -- Florian Dommert Dipl. - Phys. Institute for Computational Physics University Stuttgart Pfaffenwaldring 27 70569 Stuttgart EMail: domm...@icp.uni-stuttgart.de Homepage: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert Tel.: +49 - (0)711 - 68563613 Fax.: +49 - (0)711 - 68563658
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