RE: [gmx-users] g_dipoles - averaging
On Thu, 2011-08-04 at 15:49 +0100, Kukol, Andreas wrote: > Florian, > > I am not sure, which of the output files of g_current contains the dipole > moment for each molecule. Applying g_current to a trajectory of four > molecules of asparagin in water gives the following output: > To obtain the dipole moment for every single molecule you have to create index groups for every single molecule, and the output you are looking for is the rotational part of M contained in md.xvg the -eps flag is also not necessary and only required for the calculation of the dielectric constant. /Flo > g_current -s tpr_200ps.tpr -f xtcIRWhole_100-200ps.xtc -eps 80 -o current.xvg > (selecting 4 molecules of asparagin from the index group) > > md.xvg > @title "Averaged rotational part of M" > @xaxis label "Time (ps)" > @yaxis label "< M\sD\N > (enm)" > @TYPE xy > # time x y z average of M_D^2std.dev > 0.000 -0.10261 0.12324 0.27085 0.09908 0.31477 > 0.001 -0.10421 0.12287 0.27297 0.09977 0.31587 > 0.002 -0.09766 0.12637 0.27104 0.09951 0.31543 > ... > > dsp.xvg > @title "MSD of the squared translational dipole moment M" > @xaxis label "Time (ps)" > @yaxis label "<|M\sJ\N(t)-M\sJ\N(0)|\S2\N > / 6.0*V*k\sB\N*T / > Sm\S-1\Nps\S-1\N" > @TYPE xy > #Prefactor fit E-H: 1 / 6.0*V*k_B*T: 3.15249e-11 > 0.000 0 > 0.001 8.70985e-30 > 0.002 1.9936e-29 > ... > > mj.xvg > @title "Averaged translational part of M" > @xaxis label "Time (ps)" > @yaxis label "< M\sJ\N > (enm)" > @TYPE xy > # time x y z average of M_J^2std.dev > 0.000 0.1 0.0 0.0 0.0 0.1 > 0.001 0.1 0.0 0.0 0.0 0.1 > ... > > current.xvg was not produced due to: > ... > ... > Average volume V=32.764893 nm^3 at T=300.00 K > and corresponding refactor 1.0 / 3.0*V*k_B*T*EPSILON_0: 7.120911 > Too less points for a fit.verage volume V=32.764893 nm^3 at T=300.00 K > and corresponding refactor 1.0 / 3.0*V*k_B*T*EPSILON_0: 7.120911 > Too less points for a fit. > > I am not sure, where to find the dipole moment for each of the four molecules. > > Many thanks > Andreas > > > > -Original Message- > > From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] > > On Behalf Of Dommert Florian > > Sent: 04 August 2011 12:31 > > To: Discussion list for GROMACS users > > Subject: Re: [gmx-users] g_dipoles - averaging > > > > On Thu, 2011-08-04 at 09:08 +0100, Kukol, Andreas wrote: > > > Hello, > > > > > > Is there any way to output the dipole moment averaged over all molecules > > or for each molecule separately (and not the total dipole moment of the > > simulation box) ? > > > > > > > Yes, the tool g_current decomposes the total dipole moment into a component > > in respect to the center of mass of the molecules and a translational term, > > which is present, if you are dealing with charged species. So, if you > > prepare a corresponding index file you can derive the average molecular > > dipole moment for every molecule and finally average the results. > > > > /Flo > > > > > Apparently the dipole autocorrelation function can be obtained as an > > average over all molecules with the '-corr mol' option, but from the help > > info it is not clear, how and if the total dipole moment can be obtained in > > this way (and in which file Mtot.xvg or aver.xvg ?). > > > > > > Many thanks > > > Andreas > > > > > > > > > > > -- > > Florian Dommert > > Dipl. - Phys. > > > > Institute for Computational Physics > > University Stuttgart > > > > Pfaffenwaldring 27 > > 70569 Stuttgart > > > > EMail: domm...@icp.uni-stuttgart.de > > Homepage: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert > > > > Tel.: +49 - (0)711 - 68563613 > > Fax.: +49 - (0)711 - 68563658 > -- > 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&#x
RE: [gmx-users] g_dipoles - averaging
Florian, I am not sure, which of the output files of g_current contains the dipole moment for each molecule. Applying g_current to a trajectory of four molecules of asparagin in water gives the following output: g_current -s tpr_200ps.tpr -f xtcIRWhole_100-200ps.xtc -eps 80 -o current.xvg (selecting 4 molecules of asparagin from the index group) md.xvg @title "Averaged rotational part of M" @xaxis label "Time (ps)" @yaxis label "< M\sD\N > (enm)" @TYPE xy # time x y z average of M_D^2std.dev 0.000 -0.10261 0.12324 0.27085 0.09908 0.31477 0.001 -0.10421 0.12287 0.27297 0.09977 0.31587 0.002 -0.09766 0.12637 0.27104 0.09951 0.31543 ... dsp.xvg @title "MSD of the squared translational dipole moment M" @xaxis label "Time (ps)" @yaxis label "<|M\sJ\N(t)-M\sJ\N(0)|\S2\N > / 6.0*V*k\sB\N*T / Sm\S-1\Nps\S-1\N" @TYPE xy #Prefactor fit E-H: 1 / 6.0*V*k_B*T: 3.15249e-11 0.0000 0.001 8.70985e-30 0.002 1.9936e-29 ... mj.xvg @title "Averaged translational part of M" @xaxis label "Time (ps)" @yaxis label "< M\sJ\N > (enm)" @TYPE xy # time x y z average of M_J^2std.dev 0.0000.1 0.0 0.0 0.0 0.1 0.0010.1 0.0 0.0 0.0 0.1 ... current.xvg was not produced due to: ... ... Average volume V=32.764893 nm^3 at T=300.00 K and corresponding refactor 1.0 / 3.0*V*k_B*T*EPSILON_0: 7.120911 Too less points for a fit.verage volume V=32.764893 nm^3 at T=300.00 K and corresponding refactor 1.0 / 3.0*V*k_B*T*EPSILON_0: 7.120911 Too less points for a fit. I am not sure, where to find the dipole moment for each of the four molecules. Many thanks Andreas > -Original Message- > From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] > On Behalf Of Dommert Florian > Sent: 04 August 2011 12:31 > To: Discussion list for GROMACS users > Subject: Re: [gmx-users] g_dipoles - averaging > > On Thu, 2011-08-04 at 09:08 +0100, Kukol, Andreas wrote: > > Hello, > > > > Is there any way to output the dipole moment averaged over all molecules > or for each molecule separately (and not the total dipole moment of the > simulation box) ? > > > > Yes, the tool g_current decomposes the total dipole moment into a component > in respect to the center of mass of the molecules and a translational term, > which is present, if you are dealing with charged species. So, if you > prepare a corresponding index file you can derive the average molecular > dipole moment for every molecule and finally average the results. > > /Flo > > > Apparently the dipole autocorrelation function can be obtained as an > average over all molecules with the '-corr mol' option, but from the help > info it is not clear, how and if the total dipole moment can be obtained in > this way (and in which file Mtot.xvg or aver.xvg ?). > > > > Many thanks > > Andreas > > > > > > -- > Florian Dommert > Dipl. - Phys. > > Institute for Computational Physics > University Stuttgart > > Pfaffenwaldring 27 > 70569 Stuttgart > > EMail: domm...@icp.uni-stuttgart.de > Homepage: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert > > Tel.: +49 - (0)711 - 68563613 > Fax.: +49 - (0)711 - 68563658 -- 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_dipoles - averaging
On Thu, 2011-08-04 at 09:08 +0100, Kukol, Andreas wrote: > Hello, > > Is there any way to output the dipole moment averaged over all molecules or > for each molecule separately (and not the total dipole moment of the > simulation box) ? > Yes, the tool g_current decomposes the total dipole moment into a component in respect to the center of mass of the molecules and a translational term, which is present, if you are dealing with charged species. So, if you prepare a corresponding index file you can derive the average molecular dipole moment for every molecule and finally average the results. /Flo > Apparently the dipole autocorrelation function can be obtained as an average > over all molecules with the '-corr mol' option, but from the help info it is > not clear, how and if the total dipole moment can be obtained in this way > (and in which file Mtot.xvg or aver.xvg ?). > > Many thanks > Andreas > -- Florian Dommert Dipl. - Phys. Institute for Computational Physics University Stuttgart Pfaffenwaldring 27 70569 Stuttgart EMail: domm...@icp.uni-stuttgart.de Homepage: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert Tel.: +49 - (0)711 - 68563613 Fax.: +49 - (0)711 - 68563658 signature.asc Description: This is a digitally signed message part -- 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
