[gmx-users] g_msd Time Unit

Timothy Cholko tchol001 at ucr.edu
Wed Feb 6 03:40:37 CET 2019

Gromacs users,

When I use g_msd, I use the default time unit of 1 ps, however in the
output files it seems to be measuring MSD every 0.1 ps, and it thinks my
total trajectory is 5000 ps when it's really 50,000 ps (50 ns). This
worries me because I don't know if I can trust the exponent on the
diffusion coef that it gives me.

The trajectory has 50,000 frames and g_msd makes 50,000 MSD measurements,
but seems to think there's 1/10 ps between each measurement, when really
there's 1 ps. This output is confusing me and I can't figure out why it
seems to assume my trajectory is 5,000 ps

By the way, these are NAMD trajectories converted to .trr files, in case
that matters. Output file below:

*# g_msd -f ../../traj/fch16_50ns_nw.trr -s ../../traj/fch16.gro -o MSD_2D
-lateral z ## g_msd is part of G R O M A C S:## Great Red Oystrich Makes
All Chemists Sane#@    title "Mean Square Displacement"@    xaxis  label
"Time (ps)"@    yaxis  label "MSD (nm\S2\N)"@TYPE xy# MSD gathered over
5000 ps with 501 restarts# Diffusion constants fitted from time 500 to 4500
ps# D[       DNA] = 0.2405 (+/- 0.2415) (1e-5 cm^2/s)         0
0       0.1  0.00235535       0.2   0.0035811       0.3  0.00464145
0.4  0.00554762       0.5  0.00647601       0.6  0.00733983       0.7
0.00814599       0.8   0.0089078       0.9  0.00976139         1


More information about the gromacs.org_gmx-users mailing list