Den 2020-03-16 kl. 15:10, skrev Justin Lemkul:
On 3/16/20 10:07 AM, Joe Paul-Taylor wrote:
Hello
With running gmx msd I am told in the output the y axis unit is nm/
S2/ N, which is unexpected. Is this simply an print error or is there
an error within the calculation? I have provided a copy of the output
below, noting the units of the self-diffusion coefficient are
sensible. Any insight would be much appreciated.
The unit is correct. GROMACS does all distance calculations in terms of
nm. You get an interpreted output of the MSD in traditional units for
the diffusion constant.
The confusion maybe about the xmgrace formatting :)
nm^2 if you use the right software...
-Justin
# Created by:
# :-) GROMACS - gmx msd, 2019.2 (-:
# Command line:
# gmx msd -s topol.tpr -f npt.xtc -b 3000 -e 13000 -o
msd_IRMOF-NHPr_3OCT_8_run_1.xvg
# gmx msd is part of G R O M A C S:
#
# Gromacs Runs One Microsecond At Cannonball Speeds
#
@ title "Mean Square Displacement"
@ xaxis label "Time (ps)"
@ yaxis label "MSD (nm\S2\N)"
@TYPE xy
# MSD gathered over 10000 ps with 1001 restarts
# Diffusion constants fitted from time 1000 to 9000 ps
# D[ UNK] = 0.0031 (+/- 0.0004) (1e-5 cm^2/s)
Thank you
Joe
--
David van der Spoel, Ph.D., Professor of Biology
Head of Department, Cell & Molecular Biology, Uppsala University.
Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
http://www.icm.uu.se
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