Dear Prof.Spoel, if I do as you said, I will get only one diffusion coefficient. I want to calculate one diffusion coefficient for each 10 ns of the simulation time of 200 ns. That is, I want to get 20 diffusion values.
2013/3/28 David van der Spoel <sp...@xray.bmc.uu.se> > On 2013-03-28 10:40, Ahmet yıldırım wrote: > >> 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 >> > > Set trestart to 10001 (no restarts), or do one run with > > g_msd -f traj.xtc -s topol.top -o msd20.xvg -trestart 10000 > > > >> 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 >> >> > > -- > David van der Spoel, Ph.D., Professor of Biology > Dept. of Cell & Molec. Biol., Uppsala University. > Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. > sp...@xray.bmc.uu.se http://folding.bmc.uu.se > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > * Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<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<http://www.gromacs.org/Support/Mailing_Lists> > -- 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
