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.
-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
-- ================================================== Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com ================================================== -- 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.
