[gmx-users] g_msd with input by trjconv -pbc nojump:a concern

Ioannis Beis ibeis at mail.student.oulu.fi
Mon Mar 19 13:31:40 CET 2012

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,

More information about the gromacs.org_gmx-users mailing list