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
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