I need the trajectory of individual dipole moment of ~104 water molecules to calculate single particle dipole-dipole auto correlation function. "g_dipoles" can give dipoles of the total system or some groups (i,e solvent, sidechains, backbone) or some customised molecules (by creating .ndx files). But it is not practical to make index for each and every water molecule and run g_dipoles.
Is there any way, other than writing a code, to get the dipole moments of individual solvent molecules using GROMACS?
What water model did you use? If it's a normal, rigid additive model, all the dipole moments are the same (by definition) and are a fixed attribute of the model.
Yes I know that SPC/E waters have dipole moment ~2.35 D. But this is the magnitude. To get the Time Correlation Function I need the dipole moments as vectors inside the simulation box as well.
So you aren't after the dipole moments, you're after the components of the dipole moments. In that case, your only option is to process the trajectories molecule by molecule.
yes. so writing a code using the trajectory is faster and less tedious than processing molecule by molecule. hence I wanted to know if I can read directly from compressed trajectory.
http://www.gromacs.org/Developer_Zone/Programming_Guide/XTC_Library
That is the library you can use if writing your own code. Or just modify gmx dipoles to do what you want, which is probably easier.
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