Dear users, I used the following commands to get diffusion constants (every 10 ns) of a simulation of 100 ns . The number of frame is 5001 (write .xtc trajectory every 20 ps). I looked at RMSD vs average structure, RMSD vs starting structure, Radius of gyration, RMSD matrix. This simulation has reached to converge at last 50 ns. g_msd -f traj.xtc -s topol.tpr -o msd_1.xvg -b 0 -e 10000 g_msd -f traj.xtc -s topol.tpr -o msd_2.xvg -b 10000 -e 20000 g_msd -f traj.xtc -s topol.tpr -o msd_3.xvg -b 20000 -e 30000 ... g_msd -f traj.xtc -s topol.tpr -o msd_10.xvg -b 90000 -e 100000
1.) I used the above commands without the following flags ( -type, -lateral and -ten). Which diffusion will the above comands give? is it bulk diffusion? Gromacs manual: -type:Compute diffusion coefficient in one direction:no, x, y or z -lateral:Calculate the lateral diffusion in a plane perpendicular to: no, x, y or z -ten:Calculate the full tensor 2.) I plotted diffusions (10 values) as function of time. Diffusions dont converge. Did I do any steps by mistake? 3.) From manual: The diffusion constant is calculated by least squares fitting a straight line (D*t + c)... What is (D*t + c)? What are the meaning of D and c? 4.) What should be "Time between restarting points in trajectory"? Thanks in advance -- Ahmet Yıldırım -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
