GROMACS version:
GROMACS modification: Yes/No
Hello,
I am trying to replicate a paper where they are trying to study the effect of electric field on various factors like RMSD, radius of gyration, and dipole momnet. I am stuck at calculating the dipole momnet when induced with electric field.
this is the link to my paper: Cookie Absent
please help me in what should i do?
i used gmx dipole command but it is wrong.
gmx dipoles -f md_0_5_noPBC.xtc -s md_0_5.tpr -corr mol -o dp0.xvg
What happened? Did the command fail? Did you get some kind of incorrect output? Simply saying something is “wrong” is not specific enough for anyone to help.
You need to compute the angle yourself, from the dipole vector. Note that gmx dipoles is rather inflexible and will report the total dipole moment of everything in the topology/trajectory, so if you only want the dipole moment of the protein, you have to strip out only its information from the .tpr and trajectory files before attempting the analysis.
The output from gmx dipoles gives you the total dipole moment and its vector components. You then need to compute the angle between the electric field vector and the dipole moment vector yourself. There is no tool in GROMACS to do this.
Note that the dipole moment in the presence of an electric field will depend extremely strongly on the electrostatics method use and in particular with PME on the boundary condition at infinity (given in GROMACS by the epsilon_surface parameters). This can change the measured dipole by more than an order of magnitude. You need to understand what it is you want exactly and how electrostatics in periodic systems works.