Re: [gmx-users] g_velacc
On Thu, Jul 4, 2013 at 5:38 AM, Ishwor ishwor.poudya...@gmail.com wrote: Dear all I have calculated the diffusion coefficient using command g_msd and I want to calculate diffusion coefficient using command g_velacc. I am confused with some terms. 1I have looked the manual page of g_velacc and i found the statement the time interval between data collection points is much shorter than the time scale of the autocorrelation. What actually does that mean? Can a movie camera working a 50 frames per second show the motion of a pendulum at 50Hz? How many frames per second would you want? Mark 2I am also confused with the flag -acflen ( I have found that it describes the number of frames to be taken into consideration.Does that mean I have to take the points ,to integrate, in such a way that it matches with the time i have used in g_msd for fitting of Einsteins equation) 3 what does the flag -nonormalize indicates. Do I need to use it necessarily? 4Is the command g_analyze -f *.xvg -integrate sufficient for integration? Ishwor Nepal -- View this message in context: http://gromacs.5086.x6.nabble.com/g-velacc-tp5009541.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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
[gmx-users] g_velacc
Dear all I have calculated the diffusion coefficient using command g_msd and I want to calculate diffusion coefficient using command g_velacc. I am confused with some terms. 1I have looked the manual page of g_velacc and i found the statement the time interval between data collection points is much shorter than the time scale of the autocorrelation. What actually does that mean? 2I am also confused with the flag -acflen ( I have found that it describes the number of frames to be taken into consideration.Does that mean I have to take the points ,to integrate, in such a way that it matches with the time i have used in g_msd for fitting of Einsteins equation) 3 what does the flag -nonormalize indicates. Do I need to use it necessarily? 4Is the command g_analyze -f *.xvg -integrate sufficient for integration? Ishwor Nepal -- View this message in context: http://gromacs.5086.x6.nabble.com/g-velacc-tp5009541.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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] g_velacc
On 2013-07-04 05:38, Ishwor wrote: Dear all I have calculated the diffusion coefficient using command g_msd and I want to calculate diffusion coefficient using command g_velacc. I am confused with some terms. 1I have looked the manual page of g_velacc and i found the statement the time interval between data collection points is much shorter than the time scale of the autocorrelation. What actually does that mean? 2I am also confused with the flag -acflen ( I have found that it describes the number of frames to be taken into consideration.Does that mean I have to take the points ,to integrate, in such a way that it matches with the time i have used in g_msd for fitting of Einsteins equation) 3 what does the flag -nonormalize indicates. Do I need to use it necessarily? 4Is the command g_analyze -f *.xvg -integrate sufficient for integration? Ishwor Lots of good questions. Have you actually tried? You need to store the Velcoties quite often, maybe every 20 fs (depending on the system). Nepal -- View this message in context: http://gromacs.5086.x6.nabble.com/g-velacc-tp5009541.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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
[gmx-users] g_velacc
Hello, I am calculating the velocity auto-correlation function for my system which have 128 cation and 128 anion. How the program calculate the total velocity auto-correlation function? Does it average the velocity over all atoms at each time step? Thanks Nilesh -- 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] g_velacc
Hello, I am calculating the velocity autocorrelation function for my system. I have to calculate the g_velacc for 5 different groups within system. I have made the index file. I have also written .sh script g_velacc -f 6.trr -s 6.tpr -n glu-emi-dmp-128-no.ndx -nonormalize -o h20-vac.xvg 24 g_velacc -f 6.trr -s 6.tpr -n glu-emi-dmp-128-no.ndx -nonormalize -o h21-vac.xvg 25 g_velacc -f 6.trr -s 6.tpr -n glu-emi-dmp-128-no.ndx -nonormalize -o h24-vac.xvg 26 How can I select the group. In the above script 24, 25, 26 are the group numbers in index file. I am using Gromacs 4.0.7 version. Thanks Nilesh vac.pdf Description: Adobe PDF document -- 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] g_velacc
Nilesh Dhumal wrote: Hello, I am calculating the velocity autocorrelation function for my system. I have to calculate the g_velacc for 5 different groups within system. I have made the index file. I have also written .sh script g_velacc -f 6.trr -s 6.tpr -n glu-emi-dmp-128-no.ndx -nonormalize -o h20-vac.xvg 24 g_velacc -f 6.trr -s 6.tpr -n glu-emi-dmp-128-no.ndx -nonormalize -o h21-vac.xvg 25 g_velacc -f 6.trr -s 6.tpr -n glu-emi-dmp-128-no.ndx -nonormalize -o h24-vac.xvg 26 How can I select the group. In the above script 24, 25, 26 are the group numbers in index file. http://www.gromacs.org/Documentation/How-tos/Making_Commands_Non-Interactive -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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] g_velacc
Hello, I am trying to calculate the velocity autocorrelation function for my system. I have a system with glucose + ionic liquids (128 emi (cations) and 128 Cl (anions)). I am not getting proper velocity autocorrelation function. g_velacc -f 6.trr -s 6.tpr -n glu-emi-cl-128-no.ndx -nonormalize -e 10 -o Attached the velocity autocorrelation function. I am using Gromacs 4.0.7 version. Thanks Nilesh vac.pdf Description: Adobe PDF document -- 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] g_velacc
Hello, I am trying to calcualte the velocity autocorrelation function for my system. I have a system with glucose + ionic liquids (128 emi (cations) and 128 Cl (anions)). I am not geting proper velocity autocorrelation function. g_velacc -f 6.trr -s 6.tpr -n glu-emi-cl-128-no.ndx -nonormalize -e 10 -o Attached the velocity autocorrelation function. I am using Gromacs 4.0.7 version. Thanks Nilesh vac.pdf Description: Adobe PDF document -- 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] g_velacc
Hello, I am trying to calcualte the velocity autocorrelation function for my system. I have a system with glucose + ionic liquids (128 emi (cations) and 128 Cl (anions)). I am not geting proper velocity autocorrelation function. g_velacc -f 6.trr -s 6.tpr -n glu-emi-cl-128-no.ndx -nonormalize -e 10 -o Attached the velocity autocorrelation function. I am using Gromacs 4.0.7 version. Thanks Nilesh vac.pdf Description: Adobe PDF document -- 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] g_velacc
On 2011-05-26 22.48, Nilesh Dhumal wrote: Hello, I have calculated the velocity autocorrelation function of OH bond in glucose molecule. For this calculation I modified the index file. The modified part is pasted below. [ O10 ] 10 20 where is the hydrogen? g_velacc knows nothing about bonds just atoms. 10 is oxygen no. and 20 is oxygen. I used following command to calculate the velocity autocorrelation function. g_velacc -f 6.trr -s 6.tpr -n index.ndx -e 100 -nonormalize -o My question is how does the prog. calculate the velocity autocorrlation function. Does is subtract the velocity of hydrogen from oxygen and then calculate the autocorrelation function? I am using gromacs version 4.0.7. Thanks Nilesh -- 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] g_velacc
I am calculating OH stretching frequency by fourier transform of velocity autocorrelation function. I could calculate the OH stretching frequnecy by calculating fourier transform of OH bond. I want to know how gromacs calculate the velocity autocorrelation function of a bond (If I define a bond in index file). Does is subtract the velocity of hydrogen from oxygen and then calculate the autocorrelation function? Nilesh On Fri, May 27, 2011 2:37 am, David van der Spoel wrote: On 2011-05-26 22.48, Nilesh Dhumal wrote: Hello, I have calculated the velocity autocorrelation function of OH bond in glucose molecule. For this calculation I modified the index file. The modified part is pasted below. [ O10 ] 10 20 where is the hydrogen? g_velacc knows nothing about bonds just atoms. 10 is oxygen no. and 20 is oxygen. I used following command to calculate the velocity autocorrelation function. g_velacc -f 6.trr -s 6.tpr -n index.ndx -e 100 -nonormalize -o My question is how does the prog. calculate the velocity autocorrlation function. Does is subtract the velocity of hydrogen from oxygen and then calculate the autocorrelation function? I am using gromacs version 4.0.7. Thanks Nilesh -- 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 -- 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] g_velacc
Nilesh Dhumal wrote: I am calculating OH stretching frequency by fourier transform of velocity autocorrelation function. I could calculate the OH stretching frequnecy by calculating fourier transform of OH bond. I want to know how gromacs calculate the velocity autocorrelation function of a bond (If I define a bond in index file). Does is subtract the velocity of hydrogen from oxygen and then calculate the autocorrelation function? See manual sections 8.5.3 and 8.5.4. I doubt g_velacc does anything this complex. Check the code to be sure, but based on the equation in 8.5.4, it would seem not. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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] g_velacc
On 2011-05-27 14.26, Nilesh Dhumal wrote: I am calculating OH stretching frequency by fourier transform of velocity autocorrelation function. I could calculate the OH stretching frequnecy by calculating fourier transform of OH bond. I want to know how gromacs calculate the velocity autocorrelation function of a bond (If I define a bond in index file). Does is subtract the velocity of hydrogen from oxygen and then calculate the autocorrelation function? No, see below! There is no tool that does exactly what you want, however doing the velacc of just the hydrogen will come close. Nilesh On Fri, May 27, 2011 2:37 am, David van der Spoel wrote: On 2011-05-26 22.48, Nilesh Dhumal wrote: Hello, I have calculated the velocity autocorrelation function of OH bond in glucose molecule. For this calculation I modified the index file. The modified part is pasted below. [ O10 ] 10 20 where is the hydrogen? g_velacc knows nothing about bonds just atoms. 10 is oxygen no. and 20 is oxygen. I used following command to calculate the velocity autocorrelation function. g_velacc -f 6.trr -s 6.tpr -n index.ndx -e 100 -nonormalize -o My question is how does the prog. calculate the velocity autocorrlation function. Does is subtract the velocity of hydrogen from oxygen and then calculate the autocorrelation function? I am using gromacs version 4.0.7. Thanks Nilesh -- 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 -- 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] g_velacc
How can I calculate the velocity autocorrelation function of a bond with Gromacs? Nilesh On Fri, May 27, 2011 8:31 am, David van der Spoel wrote: On 2011-05-27 14.26, Nilesh Dhumal wrote: I am calculating OH stretching frequency by fourier transform of velocity autocorrelation function. I could calculate the OH stretching frequnecy by calculating fourier transform of OH bond. I want to know how gromacs calculate the velocity autocorrelation function of a bond (If I define a bond in index file). Does is subtract the velocity of hydrogen from oxygen and then calculate the autocorrelation function? No, see below! There is no tool that does exactly what you want, however doing the velacc of just the hydrogen will come close. Nilesh On Fri, May 27, 2011 2:37 am, David van der Spoel wrote: On 2011-05-26 22.48, Nilesh Dhumal wrote: Hello, I have calculated the velocity autocorrelation function of OH bond in glucose molecule. For this calculation I modified the index file. The modified part is pasted below. [ O10 ] 10 20 where is the hydrogen? g_velacc knows nothing about bonds just atoms. 10 is oxygen no. and 20 is oxygen. I used following command to calculate the velocity autocorrelation function. g_velacc -f 6.trr -s 6.tpr -n index.ndx -e 100 -nonormalize -o My question is how does the prog. calculate the velocity autocorrlation function. Does is subtract the velocity of hydrogen from oxygen and then calculate the autocorrelation function? I am using gromacs version 4.0.7. Thanks Nilesh -- 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 -- 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 -- 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] g_velacc
On 2011-05-27 14.39, Nilesh Dhumal wrote: How can I calculate the velocity autocorrelation function of a bond with Gromacs? READ OUR ANSWERS. Nilesh On Fri, May 27, 2011 8:31 am, David van der Spoel wrote: On 2011-05-27 14.26, Nilesh Dhumal wrote: I am calculating OH stretching frequency by fourier transform of velocity autocorrelation function. I could calculate the OH stretching frequnecy by calculating fourier transform of OH bond. I want to know how gromacs calculate the velocity autocorrelation function of a bond (If I define a bond in index file). Does is subtract the velocity of hydrogen from oxygen and then calculate the autocorrelation function? No, see below! There is no tool that does exactly what you want, however doing the velacc of just the hydrogen will come close. Nilesh On Fri, May 27, 2011 2:37 am, David van der Spoel wrote: On 2011-05-26 22.48, Nilesh Dhumal wrote: Hello, I have calculated the velocity autocorrelation function of OH bond in glucose molecule. For this calculation I modified the index file. The modified part is pasted below. [ O10 ] 10 20 where is the hydrogen? g_velacc knows nothing about bonds just atoms. 10 is oxygen no. and 20 is oxygen. I used following command to calculate the velocity autocorrelation function. g_velacc -f 6.trr -s 6.tpr -n index.ndx -e 100 -nonormalize -o My question is how does the prog. calculate the velocity autocorrlation function. Does is subtract the velocity of hydrogen from oxygen and then calculate the autocorrelation function? I am using gromacs version 4.0.7. Thanks Nilesh -- 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 -- 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 -- 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
[gmx-users] g_velacc
Hello, I have calculated the velocity autocorrelation function of OH bond in glucose molecule. For this calculation I modified the index file. The modified part is pasted below. [ O10 ] 10 20 10 is oxygen no. and 20 is oxygen. I used following command to calculate the velocity autocorrelation function. g_velacc -f 6.trr -s 6.tpr -n index.ndx -e 100 -nonormalize -o My question is how does the prog. calculate the velocity autocorrlation function. Does is subtract the velocity of hydrogen from oxygen and then calculate the autocorrelation function? I am using gromacs version 4.0.7. Thanks Nilesh -- 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] g_velacc
Hello, I am trying to calculate the velocity autocorrelation function of OH bond in glucose molecule. The calculate velocity autocorrelation function is not smooth. Its fluctuating a lot so I am geting wide/think line. Why I am not geting a smooth line? I am using gromacs version 4.0.7. Thanks Nilesh -- 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] g_velacc -mol
I'm a recent gromacs user and right now I'm starting to calculate velocity autocorrelation functions for a pure compound, using g_velacc. I'd like to know something more about the properties and consequences of the option -mol and what exactly the program does if the option is not included. I'm trying to obtain velocity autocorrelation functions for pure water for testing purposes and when the option -mol is included the system returns the message core dumped. Thanks Luis Martins -- 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] g_velacc -mol
On 2011-04-20 18.30, Luis Martins wrote: I'm a recent gromacs user and right now I'm starting to calculate velocity autocorrelation functions for a pure compound, using g_velacc. I'd like to know something more about the properties and consequences of the option -mol and what exactly the program does if the option is not included. I'm trying to obtain velocity autocorrelation functions for pure water for testing purposes and when the option -mol is included the system returns the message core dumped. Thanks Luis Martins Even if you have a correct index file? Try g_velacc -h -- 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
[gmx-users] g_velacc
Hello, I am trying to calculate the Velocity Autocorrelation Function for my system using g_velacc. I have system of 128 ionic liquids (128 cations and 128 anions). I run the trajectory for 20 ns. I used following command . g_velacc -f 3.trr -n emi-etso4-127-no.ndx -s 3.tpr -o I selected system The output file, vac.xvg, have no data. Can any one tell why its not wirting. Thanks Nilesh -- 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] g_velacc
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 On 02/01/2011 05:49 PM, Nilesh Dhumal wrote: Hello, I am trying to calculate the Velocity Autocorrelation Function for my system using g_velacc. I have system of 128 ionic liquids (128 cations and 128 anions). I run the trajectory for 20 ns. I used following command . g_velacc -f 3.trr -n emi-etso4-127-no.ndx -s 3.tpr -o I selected system The output file, vac.xvg, have no data. Can any one tell why its not wirting. Perhaps you have not velocities stored in your trr file or the index file is empty. /Flo Thanks Nilesh - -- Florian Dommert Dipl.-Phys. Institute for Computational Physics University Stuttgart Pfaffenwaldring 27 70569 Stuttgart Phone: +49(0)711/685-6-3613 Fax: +49-(0)711/685-6-3658 EMail: domm...@icp.uni-stuttgart.de Home: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.10 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iEYEARECAAYFAk1IXaQACgkQLpNNBb9GiPknNQCgyPiuIJCNofRU+wot5+E/b8be 910AoN64tjsWFhG1adFSGOYF4RBcYr2D =g8ci -END PGP SIGNATURE- -- 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] g_velacc problem
Hi Florian, in fact I had already realized that it was possible to calculate the VACF without using the -m option (although this option was important for my calculations). I have not received any attachment, have you send me something? If necessary, please, send it to my email. Following your suggestions I changed the indicated lines and recompiled the program. Now I gotta get VACF! It's working fine even including the -m flag. Thank you. eef ___ Eudes Eterno Fileti Física da Matéria Condensada Simulação Computacional de Nano-estruturas via Dinâmica Molecular -- 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] g_velacc problem
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 On 10/12/2010 11:12 PM, Eudes Fileti wrote: Hi everybody, I'm trying to use g_velacc to calculate the diffusion coeficient for my solute. For this, I performed a simple simulation to test such tool. 1000 water molecules, NPT ensemble positions and velocities colected every 0.01ps Gromacs 4.5. However, once I run: g_velacc -f traj -s -n index.ndx -o -m -acflen 1000 -nonormalize I get the following error: Group 0 ( System) has 3000 elements Group 1 (SOL) has 3000 elements Group 2 ( OW) has 1000 elements Group 3 (HW1) has 1000 elements Group 4 (HW2) has 1000 elements Select a group: 1 Selected 1: 'SOL' trn version: GMX_trn_file (single precision) Reading frame 0 time0.000 Segmentation fault Recently I used g_velacc in gmx 4.0.7 and it worked fine. Now I just tested the gmx4.5.1 version for you and it also worked. So it seems that there is something wrong with your trajectory. Are you sure that velocities were saved, which is not the case for an xtc file. You have to explicitly define nstvout in your mdp file, that tells gromacs how often the velocities should be written to the trr file. /Flo I've tried several things. I changed flag values. I tried the -mol option. I tried converting a trajectory to another format (.trj). I tried using the version 3.3.3 of g_velacc. Nothing worked, always the same error. Could someone give me a hand? Grateful eef ___ Eudes Eterno Fileti Centro de Ciências Naturais e Humanas Universidade Federal do ABC — CCNH Av. dos Estados, 5001 Santo André - SP - Brasil CEP 09210-971 http://fileti.ufabc.edu.br - -- Florian Dommert Dipl.-Phys. Institute for Computational Physics University Stuttgart Pfaffenwaldring 27 70569 Stuttgart Phone: +49(0)711/685-6-3613 Fax: +49-(0)711/685-6-3658 EMail: domm...@icp.uni-stuttgart.de Home: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.10 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iEYEARECAAYFAky1XaoACgkQLpNNBb9GiPnANQCguXrk56Thb0TmY9qJB+CKNbwH eI0An1FI0cln8dim8/Mp7qLJvE2eysI0 =Yw3G -END PGP SIGNATURE- -- 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] g_velacc problem
Hi everybody, I'm trying to use g_velacc to calculate the diffusion coeficient for my solute. For this, I performed a simple simulation to test such tool. 1000 water molecules, NPT ensemble positions and velocities colected every 0.01ps Gromacs 4.5. However, once I run: g_velacc -f traj -s -n index.ndx -o -m -acflen 1000 -nonormalize I get the following error: Group 0 ( System) has 3000 elements Group 1 (SOL) has 3000 elements Group 2 ( OW) has 1000 elements Group 3 (HW1) has 1000 elements Group 4 (HW2) has 1000 elements Select a group: 1 Selected 1: 'SOL' trn version: GMX_trn_file (single precision) Reading frame 0 time0.000 Segmentation fault I've tried several things. I changed flag values. I tried the -mol option. I tried converting a trajectory to another format (.trj). I tried using the version 3.3.3 of g_velacc. Nothing worked, always the same error. Could someone give me a hand? Grateful eef ___ Eudes Eterno Fileti Centro de Ciências Naturais e Humanas Universidade Federal do ABC — CCNH Av. dos Estados, 5001 Santo André - SP - Brasil CEP 09210-971 http://fileti.ufabc.edu.br -- 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] g_velacc problem
Hi all, I am trying to do velocity auto-correlation function(VACF) for the 'oxygen atom' present in a 63 Ang. cubic water box, simulated upto 500ps. And the velocities are stored at every 5fs. While doing the analysis(g_velacc), it got struck at 400ps, since if felt it is mainly due to the memory problem, i redid my simulation by storing the velocities at every 7fs. Now the analysis went upto 497ps and got struck after that. I tried to truncate my trajectory upto 497 by using the -trunc option from trjconv command but again i faced the same problem as before while doing analysis. Can any one help how i go about it to succeed in doing VACF. Thank you. Rama -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] g_velacc
rams rams wrote: Dear Users, I am trying to calculate the velocity correlation functions to estimate the diffusion constant of my protein which is having nearly 50 residues. I am using the following command: g_velacc -f .trr -s .tpr -n .ndx -o .xvg -fitfn exp the output is the following: COR: COR: Correlation time (plain integral from 0.000 to 2500.000 ps) = 0.90300 ps COR: Relaxation times are computed as fit to an exponential: COR: y = exp(-x/a1) COR: Fit to correlation function from 0.000 ps to 2500.000 ps, results in a COR: Fit from Integral Tail Value Sum (ps)a1 (ps) COR: 0.e+00 0.e+00 1.0458e-01 1.0458e-01 1.0458e-01 I have no idea about the output to understand. I understood it is trying to fit to the equation it displayed but have no idea about the number 0.90300 ps. The .xvg plot I got is so surprising its just a straight line parallel to time axis. I am sure I am making some mistake as I am using g_velacc for the first time. Have you zoomed in to the area close to t=0? It ssems from the integal that your ACF is pretty short. What kind of system is this? To compute a diffusion constant you don't need the expfit. From this if we want to get the Diffusion coefficient we need to integrate the correlation time from 0 to infinitive as it is described in the manual. Is there any way we can do it by using any of the options or we need to do it separately by using any other tools ? If so please let me know. I also wanted to know the following things: What does the following options do: -normalize -integrate (in g_analyze) -fitfn (there are couple of options are given if any one have idea about the sources for them ?) I calculated the diffusion coefficients using g_msd also, it gave the diffusion coefficient value as 6.0*10^-6. Which is quite large compared to the values reported in the literature which are around 2.0*10^-6. Whats going wrong here also it is not generating the output .xvg file. (It is complaining input/output fatal error). Thanks in advance, Ram. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David van der Spoel, Ph.D., Professor of Biology Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] g_velacc. Reading frame 165000 time 825.000 Killed
Vitaly Chaban wrote: Hi, I calculate the diffusion constants via Green-Kubo relation for a system of 216 molecules (5 sites in each). The velocities are saved every 0.005 ps and the total trajectory is 1000 ps long. Then applying g_velacc -nonormalize -mol -n index.ndx -acflen 1001 The process starts and after some time is killed: trn version: GMX_trn_file (single precision) Reading frame 165000 time 825.000 Killed If one gives a less part of the trajectory: 'g_velacc -nonormalize -mol -n index.ndx -acflen 1001 -b 300 -e 600' the calculation is OK. Low memory or what? It doesn't look so according to the task manager. Has anybody experienced the same problem? Any tricks to overcome it? Found on version 3.3.1. Thanks. This is typically low memory. The program reads in principle the whole trajectory in memory. You could do the analysis on half of the molecules at a time and average in xmgrace. What is a task manager? On unix systems you could check the limit command. -- David van der Spoel, Ph.D., Professor of Biology Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] g_velacc. Reading frame 165000 time 825.000 Killed
2008/8/5 David van der Spoel [EMAIL PROTECTED]: Vitaly Chaban wrote: Hi, I calculate the diffusion constants via Green-Kubo relation for a system of 216 molecules (5 sites in each). The velocities are saved every 0.005 ps and the total trajectory is 1000 ps long. Then applying g_velacc -nonormalize -mol -n index.ndx -acflen 1001 The process starts and after some time is killed: trn version: GMX_trn_file (single precision) Reading frame 165000 time 825.000 Killed If one gives a less part of the trajectory: 'g_velacc -nonormalize -mol -n index.ndx -acflen 1001 -b 300 -e 600' the calculation is OK. Low memory or what? It doesn't look so according to the task manager. Has anybody experienced the same problem? Any tricks to overcome it? Found on version 3.3.1. Thanks. This is typically low memory. The program reads in principle the whole trajectory in memory. You could do the analysis on half of the molecules at a time and average in xmgrace. Thanks for a clarification. The easy script could solve the problem. What is a task manager? On unix systems you could check the limit command. I mean xfce4-taskmanager provided with Ubuntu. -- Vitaly V. Chaban School of Chemistry National University of Kharkiv Svoboda sq., 4, Kharkiv 61077, Ukraine email: [EMAIL PROTECTED] skype: vvchaban ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] g_velacc. Reading frame 165000 time 825.000 Killed
Hi, I calculate the diffusion constants via Green-Kubo relation for a system of 216 molecules (5 sites in each). The velocities are saved every 0.005 ps and the total trajectory is 1000 ps long. Then applying g_velacc -nonormalize -mol -n index.ndx -acflen 1001 The process starts and after some time is killed: trn version: GMX_trn_file (single precision) Reading frame 165000 time 825.000 Killed If one gives a less part of the trajectory: 'g_velacc -nonormalize -mol -n index.ndx -acflen 1001 -b 300 -e 600' the calculation is OK. Low memory or what? It doesn't look so according to the task manager. Has anybody experienced the same problem? Any tricks to overcome it? Found on version 3.3.1. Thanks. -- Vitaly V. Chaban School of Chemistry National University of Kharkiv Svoboda sq., 4, Kharkiv 61077, Ukraine email: [EMAIL PROTECTED] skype: vvchaban ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
