Re: [gmx-users] RE: diffusion constant level off
- Expected values are estimated. For example İf the structure is reach to converge at last 100 ns ( all simulation time is 200 ns), then in theory, diffusion coefficients will dont change at last 100 ns. -I have only one diffusion coefficient for each 10 ns. I have 20 diffusion coefficients during all simulation time. -I controlled all msd.xvg. They are linear. The plot I sent is diffusion versus time. (Please see it again). It isnt msd vs time - I tried to increase sampling. The results are same approximately. Commands for trestart to 1000 ps: Command for 1.diffusion:g_msd -f traj.xtc -s topol.top -o msd1.xvg -trestart 1000 -beginfit -1 -endfit -1 -b 0 -e 1 # D[ Protein] = 0.1091 (+/- 0.0212) (1e-5 cm^2/s)=13.line from msd.xvg Command for 2.diffusion:g_msd -f traj.xtc -s topol.top -o msd2.xvg -trestart 1000 -beginfit -1 -endfit -1 -b 1 -e 2 # D[ Protein] = 0.0679(+/- 0.0013) (1e-5 cm^2/s) Command for 1.diffusion:g_msd -f traj.xtc -s topol.top -o msd3.xvg -trestart 1000 -beginfit -1 -endfit -1 -b 2 -e 3 ... Command for 3.diffusion:g_msd -f traj.xtc -s topol.top -o msd20.xvg -trestart 1000 -beginfit -1 -endfit -1 -b 19 -e 20 2013/3/29 Justin Lemkul jalem...@vt.edu On 3/28/13 7:56 PM, Dr. Vitaly Chaban wrote: The simplest advice is to increase sampling. I think the OP needs to describe what the system is in greater detail. For a simple liquid, I would opine that 200 ns is normally vast overkill. For a membrane, it may not be enough. There's just no way to say. -Justin -- ==**== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://www.gromacs.org/Support/Mailing_Lists -- Ahmet Yıldırım -- gmx-users mailing listgmx-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
[gmx-users] RE: diffusion constant level off
- Expected values are estimated. For example 輋 the structure is reach to converge at last 100 ns ( all simulation time is 200 ns), then in theory, diffusion coefficients will dont change at last 100 ns. -I have only one diffusion coefficient for each 10 ns. I have 20 diffusion coefficients during all simulation time. -I controlled all msd.xvg. They are linear. The plot I sent is diffusion versus time. (Please see it again). It isnt msd vs time - I tried to increase sampling. The results are same approximately. Commands for trestart to 1000 ps: Command for 1.diffusion:g_msd -f traj.xtc -s topol.top -o msd1.xvg -trestart 1000 -beginfit -1 -endfit -1 -b 0 -e 1 # D[ Protein] = 0.1091 (+/- 0.0212) (1e-5 cm^2/s)=13.line from msd.xvg Command for 2.diffusion:g_msd -f traj.xtc -s topol.top -o msd2.xvg -trestart 1000 -beginfit -1 -endfit -1 -b 1 -e 2 # D[ Protein] = 0.0679(+/- 0.0013) (1e-5 cm^2/s) Command for 1.diffusion:g_msd -f traj.xtc -s topol.top -o msd3.xvg -trestart 1000 -beginfit -1 -endfit -1 -b 2 -e 3 ... Command for 3.diffusion:g_msd -f traj.xtc -s topol.top -o msd20.xvg -trestart 1000 -beginfit -1 -endfit -1 -b 19 -e 20 2013/3/29 Justin Lemkul jalem...@vt.edu To increase sampling means to run a simulation for more nanoseconds. If your particle (protein?) is big enough, it may require a very large time to issue a proper diffusion. Therefore, the question may arise if you really want linear diffusion for this particle... Your plot is not bad. If my purpose was to assess the scale of linear diffusion, I would stop with the values you depicted. -- gmx-users mailing listgmx-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
[gmx-users] Re: diffusion constant level off
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 1 g_msd -f traj.xtc -s topol.top -o msd2.xvg -trestart 20 -beginfit -1 -endfit -1 -b 10001 -e 2 g_msd -f traj.xtc -s topol.top -o msd3.xvg -trestart 20 -beginfit -1 -endfit -1 -b 20001 -e 3 g_msd -f traj.xtc -s topol.top -o msd20.xvg -trestart 20 -beginfit -1 -endfit -1 -b 190001 -e 20 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 1 g_msd -f traj.xtc -s topol.tpr -o msd_2.xvg -b 1 -e 2 g_msd -f traj.xtc -s topol.tpr -o msd_3.xvg -b 2 -e 3 ... g_msd -f traj.xtc -s topol.tpr -o msd_10.xvg -b 9 -e 10 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 listgmx-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
Re: [gmx-users] Re: diffusion constant level off
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 1 g_msd -f traj.xtc -s topol.top -o msd2.xvg -trestart 20 -beginfit -1 -endfit -1 -b 10001 -e 2 g_msd -f traj.xtc -s topol.top -o msd3.xvg -trestart 20 -beginfit -1 -endfit -1 -b 20001 -e 3 g_msd -f traj.xtc -s topol.top -o msd20.xvg -trestart 20 -beginfit -1 -endfit -1 -b 190001 -e 20 Set trestart to 10001 (no restarts), or do one run with g_msd -f traj.xtc -s topol.top -o msd20.xvg -trestart 1 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 1 g_msd -f traj.xtc -s topol.tpr -o msd_2.xvg -b 1 -e 2 g_msd -f traj.xtc -s topol.tpr -o msd_3.xvg -b 2 -e 3 ... g_msd -f traj.xtc -s topol.tpr -o msd_10.xvg -b 9 -e 10 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.sehttp://folding.bmc.uu.se -- gmx-users mailing listgmx-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
Re: [gmx-users] Re: diffusion constant level off
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 1 g_msd -f traj.xtc -s topol.top -o msd2.xvg -trestart 20 -beginfit -1 -endfit -1 -b 10001 -e 2 g_msd -f traj.xtc -s topol.top -o msd3.xvg -trestart 20 -beginfit -1 -endfit -1 -b 20001 -e 3 g_msd -f traj.xtc -s topol.top -o msd20.xvg -trestart 20 -beginfit -1 -endfit -1 -b 190001 -e 20 Set trestart to 10001 (no restarts), or do one run with g_msd -f traj.xtc -s topol.top -o msd20.xvg -trestart 1 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 1 g_msd -f traj.xtc -s topol.tpr -o msd_2.xvg -b 1 -e 2 g_msd -f traj.xtc -s topol.tpr -o msd_3.xvg -b 2 -e 3 ... g_msd -f traj.xtc -s topol.tpr -o msd_10.xvg -b 9 -e 10 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.sehttp://folding.bmc.uu.se -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://www.gromacs.org/Support/Mailing_Lists -- Ahmet Yıldırım -- gmx-users mailing listgmx-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
[gmx-users] Re: diffusion constant level off
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 1 g_msd -f traj.xtc -s topol.top -o msd2.xvg -trestart 20 -beginfit -1 -endfit -1 -b 10001 -e 2 g_msd -f traj.xtc -s topol.top -o msd3.xvg -trestart 20 -beginfit -1 -endfit -1 -b 20001 -e 3 g_msd -f traj.xtc -s topol.top -o msd20.xvg -trestart 20 -beginfit -1 -endfit -1 -b 190001 -e 20 Set trestart to 10001 (no restarts), or do one run with g_msd -f traj.xtc -s topol.top -o msd20.xvg -trestart 1 I believe the advice was to increase trestart and you can decide yourself how much to increase. Most likely, your protein deserves better sampling than 10 ns for a linear diffusion. Dr. Vitaly Chaban -- gmx-users mailing listgmx-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
Re: [gmx-users] Re: diffusion constant level off
Dear users, Again, I have strange results (for 10,50,100,150,200 ns). I am wondering, is there a bug with g_msd? Commands for trestart to 20 ps: g_msd -f traj.xtc -s topol.top -o msd1.xvg -trestart 20 -beginfit -1 -endfit -1 -b 0 -e 1 g_msd -f traj.xtc -s topol.top -o msd2.xvg -trestart 20 -beginfit -1 -endfit -1 -b 1 -e 2 g_msd -f traj.xtc -s topol.top -o msd3.xvg -trestart 20 -beginfit -1 -endfit -1 -b 2 -e 3 ... g_msd -f traj.xtc -s topol.top -o msd20.xvg -trestart 20 -beginfit -1 -endfit -1 -b 19 -e 20 Commands for trestart to 1000 ps: g_msd -f traj.xtc -s topol.top -o msd1.xvg -trestart 1000 -beginfit -1 -endfit -1 -b 0 -e 1 g_msd -f traj.xtc -s topol.top -o msd2.xvg -trestart 1000 -beginfit -1 -endfit -1 -b 1 -e 2 g_msd -f traj.xtc -s topol.top -o msd3.xvg -trestart 1000 -beginfit -1 -endfit -1 -b 2 -e 3 ... g_msd -f traj.xtc -s topol.top -o msd20.xvg -trestart 1000 -beginfit -1 -endfit -1 -b 19 -e 20 D1 (cm^2/s):Diffusion for trestart to 20 ps D2 (cm^2/s):Diffusion for trestart to 1000 ps Time (ns) D1 D2 10 0.1616 0.1091 20 0.0735 0.0679 30 0.0775 0.0705 40 0.1097 0.1189 50 0.1471 0.1436 60 0.0468 0.048 70 0.0667 0.0652 80 0.0727 0.086 90 0.0664 0.0707 100 0.1336 0.114 110 0.0899 0.0841 120 0.0572 0.0598 130 0.0506 0.0482 140 0.0723 0.0767 150 0.1466 0.1439 160 0.0703 0.0601 170 0.081 0.0853 180 0.0278 0.027 190 0.1121 0.1024 200 0.3136 0.2981 2013/3/28 Dr. Vitaly Chaban vvcha...@gmail.com 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 1 g_msd -f traj.xtc -s topol.top -o msd2.xvg -trestart 20 -beginfit -1 -endfit -1 -b 10001 -e 2 g_msd -f traj.xtc -s topol.top -o msd3.xvg -trestart 20 -beginfit -1 -endfit -1 -b 20001 -e 3 g_msd -f traj.xtc -s topol.top -o msd20.xvg -trestart 20 -beginfit -1 -endfit -1 -b 190001 -e 20 Set trestart to 10001 (no restarts), or do one run with g_msd -f traj.xtc -s topol.top -o msd20.xvg -trestart 1 I believe the advice was to increase trestart and you can decide yourself how much to increase. Most likely, your protein deserves better sampling than 10 ns for a linear diffusion. Dr. Vitaly Chaban -- gmx-users mailing listgmx-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 -- Ahmet Yıldırım -- gmx-users mailing listgmx-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
Re: [gmx-users] Re: diffusion constant level off
perhaps, you could make a plot?? it is difficult to understand what you are speaking about. Dr. Vitaly Chaban On Thu, Mar 28, 2013 at 2:59 PM, Ahmet yıldırım ahmedo...@gmail.com wrote: Dear users, Again, I have strange results (for 10,50,100,150,200 ns). I am wondering, is there a bug with g_msd? Commands for trestart to 20 ps: g_msd -f traj.xtc -s topol.top -o msd1.xvg -trestart 20 -beginfit -1 -endfit -1 -b 0 -e 1 g_msd -f traj.xtc -s topol.top -o msd2.xvg -trestart 20 -beginfit -1 -endfit -1 -b 1 -e 2 g_msd -f traj.xtc -s topol.top -o msd3.xvg -trestart 20 -beginfit -1 -endfit -1 -b 2 -e 3 ... g_msd -f traj.xtc -s topol.top -o msd20.xvg -trestart 20 -beginfit -1 -endfit -1 -b 19 -e 20 Commands for trestart to 1000 ps: g_msd -f traj.xtc -s topol.top -o msd1.xvg -trestart 1000 -beginfit -1 -endfit -1 -b 0 -e 1 g_msd -f traj.xtc -s topol.top -o msd2.xvg -trestart 1000 -beginfit -1 -endfit -1 -b 1 -e 2 g_msd -f traj.xtc -s topol.top -o msd3.xvg -trestart 1000 -beginfit -1 -endfit -1 -b 2 -e 3 ... g_msd -f traj.xtc -s topol.top -o msd20.xvg -trestart 1000 -beginfit -1 -endfit -1 -b 19 -e 20 D1 (cm^2/s):Diffusion for trestart to 20 ps D2 (cm^2/s):Diffusion for trestart to 1000 ps Time (ns) D1 D2 10 0.1616 0.1091 20 0.0735 0.0679 30 0.0775 0.0705 40 0.1097 0.1189 50 0.1471 0.1436 60 0.0468 0.048 70 0.0667 0.0652 80 0.0727 0.086 90 0.0664 0.0707 100 0.1336 0.114 110 0.0899 0.0841 120 0.0572 0.0598 130 0.0506 0.0482 140 0.0723 0.0767 150 0.1466 0.1439 160 0.0703 0.0601 170 0.081 0.0853 180 0.0278 0.027 190 0.1121 0.1024 200 0.3136 0.2981 2013/3/28 Dr. Vitaly Chaban vvcha...@gmail.com 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 1 g_msd -f traj.xtc -s topol.top -o msd2.xvg -trestart 20 -beginfit -1 -endfit -1 -b 10001 -e 2 g_msd -f traj.xtc -s topol.top -o msd3.xvg -trestart 20 -beginfit -1 -endfit -1 -b 20001 -e 3 g_msd -f traj.xtc -s topol.top -o msd20.xvg -trestart 20 -beginfit -1 -endfit -1 -b 190001 -e 20 Set trestart to 10001 (no restarts), or do one run with g_msd -f traj.xtc -s topol.top -o msd20.xvg -trestart 1 I believe the advice was to increase trestart and you can decide yourself how much to increase. Most likely, your protein deserves better sampling than 10 ns for a linear diffusion. Dr. Vitaly Chaban -- gmx-users mailing listgmx-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 -- Ahmet Yıldırım -- gmx-users mailing listgmx-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
Re: [gmx-users] Re: diffusion constant level off
On Thu, Mar 28, 2013 at 9:59 AM, Ahmet yıldırım ahmedo...@gmail.com wrote: Dear users, Again, I have strange results (for 10,50,100,150,200 ns). I am wondering, is there a bug with g_msd? I see no evidence for a bug, and you should avoid such speculation unless you know exactly how the program should behave. Only then, after an analysis of known quantities or behavior, can we discuss bugginess. Do you know how g_msd works? Do you know what all of the flags are doing, or are you just making adjustments hoping for clarity? You may find the following post very illuminating: http://lists.gromacs.org/pipermail/gmx-users/2010-July/052512.html -Justin Commands for trestart to 20 ps: g_msd -f traj.xtc -s topol.top -o msd1.xvg -trestart 20 -beginfit -1 -endfit -1 -b 0 -e 1 g_msd -f traj.xtc -s topol.top -o msd2.xvg -trestart 20 -beginfit -1 -endfit -1 -b 1 -e 2 g_msd -f traj.xtc -s topol.top -o msd3.xvg -trestart 20 -beginfit -1 -endfit -1 -b 2 -e 3 ... g_msd -f traj.xtc -s topol.top -o msd20.xvg -trestart 20 -beginfit -1 -endfit -1 -b 19 -e 20 Commands for trestart to 1000 ps: g_msd -f traj.xtc -s topol.top -o msd1.xvg -trestart 1000 -beginfit -1 -endfit -1 -b 0 -e 1 g_msd -f traj.xtc -s topol.top -o msd2.xvg -trestart 1000 -beginfit -1 -endfit -1 -b 1 -e 2 g_msd -f traj.xtc -s topol.top -o msd3.xvg -trestart 1000 -beginfit -1 -endfit -1 -b 2 -e 3 ... g_msd -f traj.xtc -s topol.top -o msd20.xvg -trestart 1000 -beginfit -1 -endfit -1 -b 19 -e 20 D1 (cm^2/s):Diffusion for trestart to 20 ps D2 (cm^2/s):Diffusion for trestart to 1000 ps Time (ns) D1 D2 10 0.1616 0.1091 20 0.0735 0.0679 30 0.0775 0.0705 40 0.1097 0.1189 50 0.1471 0.1436 60 0.0468 0.048 70 0.0667 0.0652 80 0.0727 0.086 90 0.0664 0.0707 100 0.1336 0.114 110 0.0899 0.0841 120 0.0572 0.0598 130 0.0506 0.0482 140 0.0723 0.0767 150 0.1466 0.1439 160 0.0703 0.0601 170 0.081 0.0853 180 0.0278 0.027 190 0.1121 0.1024 200 0.3136 0.2981 2013/3/28 Dr. Vitaly Chaban vvcha...@gmail.com 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 1 g_msd -f traj.xtc -s topol.top -o msd2.xvg -trestart 20 -beginfit -1 -endfit -1 -b 10001 -e 2 g_msd -f traj.xtc -s topol.top -o msd3.xvg -trestart 20 -beginfit -1 -endfit -1 -b 20001 -e 3 g_msd -f traj.xtc -s topol.top -o msd20.xvg -trestart 20 -beginfit -1 -endfit -1 -b 190001 -e 20 Set trestart to 10001 (no restarts), or do one run with g_msd -f traj.xtc -s topol.top -o msd20.xvg -trestart 1 I believe the advice was to increase trestart and you can decide yourself how much to increase. Most likely, your protein deserves better sampling than 10 ns for a linear diffusion. Dr. Vitaly Chaban -- gmx-users mailing listgmx-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 -- Ahmet Yıldırım -- gmx-users mailing listgmx-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 -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-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
Re: [gmx-users] Re: diffusion constant level off
Please see plot: http://imageshack.us/photo/my-images/35/diffusion.png/ 2013/3/28 Justin Lemkul jalem...@vt.edu On Thu, Mar 28, 2013 at 9:59 AM, Ahmet yıldırım ahmedo...@gmail.com wrote: Dear users, Again, I have strange results (for 10,50,100,150,200 ns). I am wondering, is there a bug with g_msd? I see no evidence for a bug, and you should avoid such speculation unless you know exactly how the program should behave. Only then, after an analysis of known quantities or behavior, can we discuss bugginess. Do you know how g_msd works? Do you know what all of the flags are doing, or are you just making adjustments hoping for clarity? You may find the following post very illuminating: http://lists.gromacs.org/pipermail/gmx-users/2010-July/052512.html -Justin Commands for trestart to 20 ps: g_msd -f traj.xtc -s topol.top -o msd1.xvg -trestart 20 -beginfit -1 -endfit -1 -b 0 -e 1 g_msd -f traj.xtc -s topol.top -o msd2.xvg -trestart 20 -beginfit -1 -endfit -1 -b 1 -e 2 g_msd -f traj.xtc -s topol.top -o msd3.xvg -trestart 20 -beginfit -1 -endfit -1 -b 2 -e 3 ... g_msd -f traj.xtc -s topol.top -o msd20.xvg -trestart 20 -beginfit -1 -endfit -1 -b 19 -e 20 Commands for trestart to 1000 ps: g_msd -f traj.xtc -s topol.top -o msd1.xvg -trestart 1000 -beginfit -1 -endfit -1 -b 0 -e 1 g_msd -f traj.xtc -s topol.top -o msd2.xvg -trestart 1000 -beginfit -1 -endfit -1 -b 1 -e 2 g_msd -f traj.xtc -s topol.top -o msd3.xvg -trestart 1000 -beginfit -1 -endfit -1 -b 2 -e 3 ... g_msd -f traj.xtc -s topol.top -o msd20.xvg -trestart 1000 -beginfit -1 -endfit -1 -b 19 -e 20 D1 (cm^2/s):Diffusion for trestart to 20 ps D2 (cm^2/s):Diffusion for trestart to 1000 ps Time (ns) D1 D2 10 0.1616 0.1091 20 0.0735 0.0679 30 0.0775 0.0705 40 0.1097 0.1189 50 0.1471 0.1436 60 0.0468 0.048 70 0.0667 0.0652 80 0.0727 0.086 90 0.0664 0.0707 100 0.1336 0.114 110 0.0899 0.0841 120 0.0572 0.0598 130 0.0506 0.0482 140 0.0723 0.0767 150 0.1466 0.1439 160 0.0703 0.0601 170 0.081 0.0853 180 0.0278 0.027 190 0.1121 0.1024 200 0.3136 0.2981 2013/3/28 Dr. Vitaly Chaban vvcha...@gmail.com 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 1 g_msd -f traj.xtc -s topol.top -o msd2.xvg -trestart 20 -beginfit -1 -endfit -1 -b 10001 -e 2 g_msd -f traj.xtc -s topol.top -o msd3.xvg -trestart 20 -beginfit -1 -endfit -1 -b 20001 -e 3 g_msd -f traj.xtc -s topol.top -o msd20.xvg -trestart 20 -beginfit -1 -endfit -1 -b 190001 -e 20 Set trestart to 10001 (no restarts), or do one run with g_msd -f traj.xtc -s topol.top -o msd20.xvg -trestart 1 I believe the advice was to increase trestart and you can decide yourself how much to increase. Most likely, your protein deserves better sampling than 10 ns for a linear diffusion. Dr. Vitaly Chaban -- gmx-users mailing listgmx-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 -- Ahmet Yıldırım -- gmx-users mailing listgmx-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 -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-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
[gmx-users] RE: diffusion constant level off
The simplest advice is to increase sampling. Please see plot: http://imageshack.us/photo/my-images/35/diffusion.png/ 2013/3/28 Justin Lemkul jalem...@vt.edu On Thu, Mar 28, 2013 at 9:59 AM, Ahmet yıldırım ahmedo...@gmail.com wrote: Dear users, Again, I have strange results (for 10,50,100,150,200 ns). I am wondering, is there a bug with g_msd? I see no evidence for a bug, and you should avoid such speculation unless you know exactly how the program should behave. Only then, after an analysis of known quantities or behavior, can we discuss bugginess. Do you know how g_msd works? Do you know what all of the flags are doing, or are you just making adjustments hoping for clarity? You may find the following post very illuminating: http://lists.gromacs.org/pipermail/gmx-users/2010-July/052512.html -Justin Commands for trestart to 20 ps: g_msd -f traj.xtc -s topol.top -o msd1.xvg -trestart 20 -beginfit -1 -endfit -1 -b 0 -e 1 g_msd -f traj.xtc -s topol.top -o msd2.xvg -trestart 20 -beginfit -1 -endfit -1 -b 1 -e 2 g_msd -f traj.xtc -s topol.top -o msd3.xvg -trestart 20 -beginfit -1 -endfit -1 -b 2 -e 3 ... g_msd -f traj.xtc -s topol.top -o msd20.xvg -trestart 20 -beginfit -1 -endfit -1 -b 19 -e 20 Commands for trestart to 1000 ps: g_msd -f traj.xtc -s topol.top -o msd1.xvg -trestart 1000 -beginfit -1 -endfit -1 -b 0 -e 1 g_msd -f traj.xtc -s topol.top -o msd2.xvg -trestart 1000 -beginfit -1 -endfit -1 -b 1 -e 2 g_msd -f traj.xtc -s topol.top -o msd3.xvg -trestart 1000 -beginfit -1 -endfit -1 -b 2 -e 3 ... g_msd -f traj.xtc -s topol.top -o msd20.xvg -trestart 1000 -beginfit -1 -endfit -1 -b 19 -e 20 D1 (cm^2/s):Diffusion for trestart to 20 ps D2 (cm^2/s):Diffusion for trestart to 1000 ps Time (ns) D1 D2 10 0.1616 0.1091 20 0.0735 0.0679 30 0.0775 0.0705 40 0.1097 0.1189 50 0.1471 0.1436 60 0.0468 0.048 70 0.0667 0.0652 80 0.0727 0.086 90 0.0664 0.0707 100 0.1336 0.114 110 0.0899 0.0841 120 0.0572 0.0598 130 0.0506 0.0482 140 0.0723 0.0767 150 0.1466 0.1439 160 0.0703 0.0601 170 0.081 0.0853 180 0.0278 0.027 190 0.1121 0.1024 200 0.3136 0.2981 2013/3/28 Dr. Vitaly Chaban vvcha...@gmail.com 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 1 g_msd -f traj.xtc -s topol.top -o msd2.xvg -trestart 20 -beginfit -1 -endfit -1 -b 10001 -e 2 g_msd -f traj.xtc -s topol.top -o msd3.xvg -trestart 20 -beginfit -1 -endfit -1 -b 20001 -e 3 g_msd -f traj.xtc -s topol.top -o msd20.xvg -trestart 20 -beginfit -1 -endfit -1 -b 190001 -e 20 Set trestart to 10001 (no restarts), or do one run with g_msd -f traj.xtc -s topol.top -o msd20.xvg -trestart 1 I believe the advice was to increase trestart and you can decide yourself how much to increase. Most likely, your protein deserves better sampling than 10 ns for a linear diffusion. Dr. Vitaly Chaban -- gmx-users mailing listgmx-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
Re: [gmx-users] Re: diffusion constant level off
On 3/28/13 5:32 PM, Ahmet yıldırım wrote: Please see plot: http://imageshack.us/photo/my-images/35/diffusion.png/ How did you come up with your expected values? What does the original msd.xvg plot look like? It should be basically linear. If it's not, then you have found the source of your problem. -Justin 2013/3/28 Justin Lemkul jalem...@vt.edu On Thu, Mar 28, 2013 at 9:59 AM, Ahmet yıldırım ahmedo...@gmail.com wrote: Dear users, Again, I have strange results (for 10,50,100,150,200 ns). I am wondering, is there a bug with g_msd? I see no evidence for a bug, and you should avoid such speculation unless you know exactly how the program should behave. Only then, after an analysis of known quantities or behavior, can we discuss bugginess. Do you know how g_msd works? Do you know what all of the flags are doing, or are you just making adjustments hoping for clarity? You may find the following post very illuminating: http://lists.gromacs.org/pipermail/gmx-users/2010-July/052512.html -Justin Commands for trestart to 20 ps: g_msd -f traj.xtc -s topol.top -o msd1.xvg -trestart 20 -beginfit -1 -endfit -1 -b 0 -e 1 g_msd -f traj.xtc -s topol.top -o msd2.xvg -trestart 20 -beginfit -1 -endfit -1 -b 1 -e 2 g_msd -f traj.xtc -s topol.top -o msd3.xvg -trestart 20 -beginfit -1 -endfit -1 -b 2 -e 3 ... g_msd -f traj.xtc -s topol.top -o msd20.xvg -trestart 20 -beginfit -1 -endfit -1 -b 19 -e 20 Commands for trestart to 1000 ps: g_msd -f traj.xtc -s topol.top -o msd1.xvg -trestart 1000 -beginfit -1 -endfit -1 -b 0 -e 1 g_msd -f traj.xtc -s topol.top -o msd2.xvg -trestart 1000 -beginfit -1 -endfit -1 -b 1 -e 2 g_msd -f traj.xtc -s topol.top -o msd3.xvg -trestart 1000 -beginfit -1 -endfit -1 -b 2 -e 3 ... g_msd -f traj.xtc -s topol.top -o msd20.xvg -trestart 1000 -beginfit -1 -endfit -1 -b 19 -e 20 D1 (cm^2/s):Diffusion for trestart to 20 ps D2 (cm^2/s):Diffusion for trestart to 1000 ps Time (ns) D1 D2 10 0.1616 0.1091 20 0.0735 0.0679 30 0.0775 0.0705 40 0.1097 0.1189 50 0.1471 0.1436 60 0.0468 0.048 70 0.0667 0.0652 80 0.0727 0.086 90 0.0664 0.0707 100 0.1336 0.114 110 0.0899 0.0841 120 0.0572 0.0598 130 0.0506 0.0482 140 0.0723 0.0767 150 0.1466 0.1439 160 0.0703 0.0601 170 0.081 0.0853 180 0.0278 0.027 190 0.1121 0.1024 200 0.3136 0.2981 2013/3/28 Dr. Vitaly Chaban vvcha...@gmail.com 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 1 g_msd -f traj.xtc -s topol.top -o msd2.xvg -trestart 20 -beginfit -1 -endfit -1 -b 10001 -e 2 g_msd -f traj.xtc -s topol.top -o msd3.xvg -trestart 20 -beginfit -1 -endfit -1 -b 20001 -e 3 g_msd -f traj.xtc -s topol.top -o msd20.xvg -trestart 20 -beginfit -1 -endfit -1 -b 190001 -e 20 Set trestart to 10001 (no restarts), or do one run with g_msd -f traj.xtc -s topol.top -o msd20.xvg -trestart 1 I believe the advice was to increase trestart and you can decide yourself how much to increase. Most likely, your protein deserves better sampling than 10 ns for a linear diffusion. Dr. Vitaly Chaban -- gmx-users mailing listgmx-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 -- Ahmet Yıldırım -- gmx-users mailing listgmx-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 -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-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
Re: [gmx-users] RE: diffusion constant level off
On 3/28/13 7:56 PM, Dr. Vitaly Chaban wrote: The simplest advice is to increase sampling. I think the OP needs to describe what the system is in greater detail. For a simple liquid, I would opine that 200 ns is normally vast overkill. For a membrane, it may not be enough. There's just no way to say. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-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
