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 0.0103875* Thanks, Tim -- 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.
