[gmx-users] how to use g_dipoles
dear users: I am using Gromacs 4.0.5. My system consist of chared plain and charged protein. How can i use the g_dipoles to get the protein's dipole? what is the exact option? Thanks! Lee -- 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_dipoles with net charge
Dear gmx users: I am using gms 4.07, my system contains a protein with net charge and a plain,here I want to calculate the the angle between the dipoles of protein and the XY plain vs. time. What should I do? And is this way right: I define a positive center and a negative center, and define a vector which point from the negative center to the positive center, and the angle between the vector and the plain is what I want? Or the “g_dipoles” command is exactly doing the way I mentioned before? If so ,please tell me the details on how to get the results use this command! Thanks a lot! Li -- 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] PME energy calculation
Hello Everyone, I am using PME(4.05) to calculate the long-rang electrostatic interaction, but when I finished the Simulation, I found that I can’t get the result of energy of the part of “fourier space（long range part）”. In other word，there is only a congregation of energy of that named Coul. recip. Is there any way that I can get the energy of “group to group” of the “fourier space” ? Thanks! Li -- 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
