Re: [gmx-users] Temperature Histogram
On 11/20/12 2:13 AM, cuong nguyen wrote: Dear, Thanks a lot for your suggestion Justin. I have a box 3 3 20 and want to plot the temperature along the z axis. I did the commands: g_energy -f NVT_20ns.edr -s topol.top -o temp g_analyze -f temp.xvg -dist temp.xvg and got the results: 281.9 0 282 0.000149997 282.1 0 282.2 0 282.3 0 282.4 0 282.5 0 282.6 0 282.7 0 282.8 0 282.9 0 283 0 283.1 0 283.2 0 283.3 0 283.4 0 283.5 0 283.6 0 283.7 0.000149997 283.8 0 283.9 0 284 0 284.1 0.000149997 284.2 0 284.3 0.000149997 . I supposed the first column should start from 0 to 20. Please tell me what's wrong I am doing? g_energy does not plot quantities as a function of box length. -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
Re: [gmx-users] Temperature Histogram
Dear, Thanks a lot for your suggestion Justin. I have a box 3 3 20 and want to plot the temperature along the z axis. I did the commands: g_energy -f NVT_20ns.edr -s topol.top -o temp g_analyze -f temp.xvg -dist temp.xvg and got the results: 281.9 0 282 0.000149997 282.1 0 282.2 0 282.3 0 282.4 0 282.5 0 282.6 0 282.7 0 282.8 0 282.9 0 283 0 283.1 0 283.2 0 283.3 0 283.4 0 283.5 0 283.6 0 283.7 0.000149997 283.8 0 283.9 0 284 0 284.1 0.000149997 284.2 0 284.3 0.000149997 . I supposed the first column should start from 0 to 20. Please tell me what's wrong I am doing? Best regards, Cuong On 8 November 2012 01:16, Justin Lemkul jalem...@vt.edu wrote: On 11/7/12 11:42 AM, Samadashvili Nino wrote: Hello, I would like to calculate temperature in my system along the axis. Could you please tell me if there is a way to make a temperature histogram with Gromacs? Use g_energy to extract temperatures from the .edr file, then g_analyze -dist on that .xvg file. -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 -- 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] Temperature Histogram
Thank you for your answer. However, when I use g_energy on .edr file it prints the average temperature of the system and not of the group of atoms that I am interested in, which is why I was trying to make g_traj work cos it uses index.ndx file for choosing the segment from your system and calculate the average temperature for that segment. One more thing, g_energy has Pres-XX, XY etc., what are these? Cheers, Nino From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Justin Lemkul [jalem...@vt.edu] Sent: Wednesday, November 14, 2012 2:18 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Temperature Histogram On 11/14/12 7:10 AM, Samadashvili Nino wrote: Dear Justin, I have been looking for some option to calculate the average temperature, locally in my system. I found g_traj which I can use with index file and calculate temperature for a particular group in my system but somehow it gives a wrong value (The average temperature (NVT simulation) is 240 K and g_traj outputs 120 K). Is there any other option available in Gromacs? g_traj doesn't account for constraints, but the result can be calculated from what g_traj produces. That's more complicated than you need, and will not be accurate over all MD steps. All you need to do is extract the temperatures from the .edr file using g_energy and the average is printed to the screen. This average is correct over all steps, since energy history is stored in the .edr file and is not limited to nst* output. -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-- 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] Temperature Histogram
Dear Justin, I have been looking for some option to calculate the average temperature, locally in my system. I found g_traj which I can use with index file and calculate temperature for a particular group in my system but somehow it gives a wrong value (The average temperature (NVT simulation) is 240 K and g_traj outputs 120 K). Is there any other option available in Gromacs? Thank you for your attention. Cheers, Nino From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Justin Lemkul [jalem...@vt.edu] Sent: Wednesday, November 07, 2012 7:16 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Temperature Histogram On 11/7/12 11:42 AM, Samadashvili Nino wrote: Hello, I would like to calculate temperature in my system along the axis. Could you please tell me if there is a way to make a temperature histogram with Gromacs? Use g_energy to extract temperatures from the .edr file, then g_analyze -dist on that .xvg file. -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 -- 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] Temperature Histogram
On 11/14/12 7:10 AM, Samadashvili Nino wrote: Dear Justin, I have been looking for some option to calculate the average temperature, locally in my system. I found g_traj which I can use with index file and calculate temperature for a particular group in my system but somehow it gives a wrong value (The average temperature (NVT simulation) is 240 K and g_traj outputs 120 K). Is there any other option available in Gromacs? g_traj doesn't account for constraints, but the result can be calculated from what g_traj produces. That's more complicated than you need, and will not be accurate over all MD steps. All you need to do is extract the temperatures from the .edr file using g_energy and the average is printed to the screen. This average is correct over all steps, since energy history is stored in the .edr file and is not limited to nst* output. -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
[gmx-users] Temperature Histogram
Hello, I would like to calculate temperature in my system along the axis. Could you please tell me if there is a way to make a temperature histogram with Gromacs? Thank you for your attention. Cheers, Nino-- 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] Temperature Histogram
On 11/7/12 11:42 AM, Samadashvili Nino wrote: Hello, I would like to calculate temperature in my system along the axis. Could you please tell me if there is a way to make a temperature histogram with Gromacs? Use g_energy to extract temperatures from the .edr file, then g_analyze -dist on that .xvg file. -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
