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^2 std.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^2 std.dev 0.000 0.00001 0.00000 0.00000 0.00000 0.00001 0.001 0.00001 0.00000 0.00000 0.00000 0.00001 ... current.xvg was not produced due to: ... ... Average volume V=32.764893 nm^3 at T=300.000000 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=300.000000 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
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