Dear users, This time, I calculated the diffusion coefficients of protein for each 10 ns of the simulation providing a total simulation time of 200 ns. g_msd -f traj.xtc -s topol.top -o msd1.xvg -trestart 20 -beginfit -1 -endfit -1 -b 0 -e 10000 g_msd -f traj.xtc -s topol.top -o msd2.xvg -trestart 20 -beginfit -1 -endfit -1 -b 10001 -e 20000 g_msd -f traj.xtc -s topol.top -o msd3.xvg -trestart 20 -beginfit -1 -endfit -1 -b 20001 -e 30000 .... g_msd -f traj.xtc -s topol.top -o msd20.xvg -trestart 20 -beginfit -1 -endfit -1 -b 190001 -e 200000
I have strange Diffusion results (especially 10,50,100,150,200 ns). How can I fix this problem? Results: Time (ns) D(cm^2/s) 10 0.1616 20 0.0735 30 0.0775 40 0.1097 50 0.1471 60 0.0468 70 0.0667 80 0.0727 90 0.0664 100 0.1336 110 0.0899 120 0.0572 130 0.0506 140 0.0723 150 0.1466 160 0.0703 170 0.081 180 0.0278 190 0.1121 200 0.3136 2013/3/27 Ahmet yıldırım <ahmedo...@gmail.com> > > 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 -- 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
