Hi,
I am using GROMACS V-5.1.4. In my system, I have two slabs mirroring each other and some water molecules in between the slabs. The normal to the slab is X-Axis.
I would like to calculated the water dipole orientation normal to the surface. gmx_d h2order can calculate the dipole moment only in Z-direction (limitation of the C++ code). It could not be able to calculate and plot the dipole resolved along X and Y dimensions of box. However, my slab has normal to X axis.
Does anyone have any idea how to deal with that?
Another solution might be to interchange the X and Z coordinates of entire trajectory file so that my Z becomes X and X becomes Z. Then I can easily calculate dipole along z direction.
Does anyone know how to rotate the trajectory in GROMACS?
Rotates the trajectory by a given angle on a given axis. The axis is defined by the user, combining the direction vector and a point. This point can be the center of geometry or the center of mass of a user defined AtomGroup, or an array defining custom coordinates.
For further information please check this link
https://www.mdanalysis.org/docs/documentation_pages/transformations/rotate.html
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