GROMACS version: 2020.1-Ubuntu-2020.1-1
GROMACS modification: Yes/No
I am trying to calculate the dipole moment of a protein ( actually my system is lysozyme in water, as given in the tutorial of gromacs). During the production MD step, I applied certain electric field to the protein, it is unfolded little bit, but still within the water box. when i have tried to calculate the dipole moment , i got an error as
Fatal error:
Due to new ways of treating molecules in GROMACS the total dipole in the
energy file may be incorrect, because molecules can be split over periodic
boundary conditions before computing the dipole. Please use your trajectory
file.
please guide me to solve this issue.
The error means you need to compute the dipole from a PBC-corrected trajectory file to ensure that the group of interest is “whole” within the central image.
I don’t know what you will obtain from this value aside from a reflection of what you already know. Any apparent change in dipole moment has nothing to do with changes in electronic structure when using an additive force field. Any change you see just means the nuclear coordinates changed in some way, which it sounds like you already know (partial unfolding).
Hello sir,
My problem solved after correcting my xtc and gro file for PBC. Next, after running gmx dipole, I obtained the dipole moments (x , y, z components for each time frame) as xvg file and also the total Dipole moment displayed on screen.
But when i have tried to visualize it along with my proten in vmd using dip watcher plugin, i failed. And it is obvious, since my gro file does not carry chatge information.
What is the way to visualize this calculated dipole moment along with protein ??
Thank you very much
