[gmx-users] Calculation of Temperature of Cluster
Dear All, I tried to use g_clustsize_d program for estimation of temperature of cluster/nanodroplet but the temperature output file is empty. Could you comment where is the problem? Please note that I can get Temperature of system using g_energy_d but I'm interest to know cooling effect of nano-drop after evaporation. Best Rasoul -- 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] Calculation of Temperature of Cluster
On Mon, Apr 8, 2013 at 9:01 AM, Rasoul Nasiri nasiri1...@gmail.com wrote: Dear All, I tried to use g_clustsize_d program for estimation of temperature of cluster/nanodroplet but the temperature output file is empty. Could you comment where is the problem? Not without seeing your command line. I'd be willing to guess that you either used an .xtc file (which does not store velocities) or a .trr that didn't save velocities (i.e. nstvout = 0). -Justin Please note that I can get Temperature of system using g_energy_d but I'm interest to know cooling effect of nano-drop after evaporation. Best Rasoul -- 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] Calculation of Temperature of Cluster
Bellow is my command which I used: g_clustsize_d -f traj.xtc -s topol.tpr -n n.ndx -nc nclust.xvg -mc maxclust .xvg -ac avclust.xvg -mcn maxclust.ndx -cut 0.516 -temp Tempe.xvg Rasoul On Mon, Apr 8, 2013 at 2:04 PM, Justin Lemkul jalem...@vt.edu wrote: On Mon, Apr 8, 2013 at 9:01 AM, Rasoul Nasiri nasiri1...@gmail.com wrote: Dear All, I tried to use g_clustsize_d program for estimation of temperature of cluster/nanodroplet but the temperature output file is empty. Could you comment where is the problem? Not without seeing your command line. I'd be willing to guess that you either used an .xtc file (which does not store velocities) or a .trr that didn't save velocities (i.e. nstvout = 0). -Justin Please note that I can get Temperature of system using g_energy_d but I'm interest to know cooling effect of nano-drop after evaporation. Best Rasoul -- 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 -- 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] Calculation of Temperature of Cluster
On Mon, Apr 8, 2013 at 9:08 AM, Rasoul Nasiri nasiri1...@gmail.com wrote: Bellow is my command which I used: g_clustsize_d -f traj.xtc -s topol.tpr -n n.ndx -nc nclust.xvg -mc maxclust .xvg -ac avclust.xvg -mcn maxclust.ndx -cut 0.516 -temp Tempe.xvg Then it is exactly what I said. Temperatures require velocities. Velocities are not stored in .xtc files and thus you can't extract any temperature information in this way. -Justin -- 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] Calculation of Temperature of Cluster
Justin, Thanks for your comment. Instead of .xtc, I just used .trr in which nstvout isn’t zero. I'm still encountering to empty file for temperature. Rasoul On Mon, Apr 8, 2013 at 2:10 PM, Justin Lemkul jalem...@vt.edu wrote: On Mon, Apr 8, 2013 at 9:08 AM, Rasoul Nasiri nasiri1...@gmail.com wrote: Bellow is my command which I used: g_clustsize_d -f traj.xtc -s topol.tpr -n n.ndx -nc nclust.xvg -mc maxclust .xvg -ac avclust.xvg -mcn maxclust.ndx -cut 0.516 -temp Tempe.xvg Then it is exactly what I said. Temperatures require velocities. Velocities are not stored in .xtc files and thus you can't extract any temperature information in this way. -Justin -- 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 -- 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] Calculation of Temperature of Cluster
On Mon, Apr 8, 2013 at 9:24 AM, Rasoul Nasiri nasiri1...@gmail.com wrote: Justin, Thanks for your comment. Instead of .xtc, I just used .trr in which nstvout isn’t zero. I'm still encountering to empty file for temperature. Can you please provide the gmxcheck output for the .trr file? I suppose there could be a bug, but we need to rule out a few things first. If g_clustsize still fails, you can get the output temperature from g_traj -ot, which appears to have a redundant function. -Justin -- 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] Calculation of Temperature of Cluster
One suggestion, Is there any chance to retrieve trajectory of un-evaporated molecules using one of gromacs tools? Now I have a ndx file which show number of atoms stayed in drop, Which one is better? I mean if I can get trajectory (position+velocity) unevaporated molecules, I would be able estimate the temperature as well. Is it correct? Rasoul On Mon, Apr 8, 2013 at 2:30 PM, Justin Lemkul jalem...@vt.edu wrote: On Mon, Apr 8, 2013 at 9:24 AM, Rasoul Nasiri nasiri1...@gmail.com wrote: Justin, Thanks for your comment. Instead of .xtc, I just used .trr in which nstvout isn’t zero. I'm still encountering to empty file for temperature. Can you please provide the gmxcheck output for the .trr file? I suppose there could be a bug, but we need to rule out a few things first. If g_clustsize still fails, you can get the output temperature from g_traj -ot, which appears to have a redundant function. -Justin -- 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 -- 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] Calculation of Temperature of Cluster
On Mon, Apr 8, 2013 at 9:39 AM, Rasoul Nasiri nasiri1...@gmail.com wrote: One suggestion, Is there any chance to retrieve trajectory of un-evaporated molecules using one of gromacs tools? Now I have a ndx file which show number of atoms stayed in drop, Sure, that's what trjconv does. Which one is better? I mean if I can get trajectory (position+velocity) unevaporated molecules, I would be able estimate the temperature as well. Is it correct? I suppose so. You can (in theory) use g_traj or g_clustsize to extract temperature, and the analyzed atoms can be chosen as an index group of a larger system or simply that subset that has already been parsed out of the trajetory. Either approach should be equivalent. -Justin -- 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
