Thank you Justin and David, that's very helpful 😊
-----Original Message----- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <gromacs.org_gmx-users-boun...@maillist.sys.kth.se> On Behalf Of David van der Spoel Sent: 16 March 2020 17:13 To: gmx-us...@gromacs.org Subject: Re: [gmx-users] gmx msd unusual unit CAUTION: This email came from outside of the University. To keep your account safe, only click on links and open attachments if you know the person who sent the email, or you expected to receive this communication. 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[Â Â Â Â Â Â 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 -- 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. -- 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.