GMX-SPOL(1)

📦
version 2026.4 · 8 versions
, in nixpkgs unstable, ubuntu stonking

🦋 NAME 🦋

hi bestie 💖 welcome to GMX-SPOL(1), the GROMACS manpage for gmx-spol — and what does it do, you ask?

gmx-spol — analyze solvent dipole orientation and polarization around solutes ✨

🌸 SYNOPSIS 🌸

okay so here's the whole summoning ritual, copy it exactly, no cap:

   gmx spol [-f [<.xtc/.trr/...>]] [-s [<.tpr>]] [-n [<.ndx>]]
            [-o [<.xvg>]] [-b <time>] [-e <time>] [-dt <time>] [-[no]w]
            [-xvg <enum>] [-[no]com] [-refat <int>] [-rmin <real>]
            [-rmax <real>] [-dip <real>] [-bw <real>]

🫶 DESCRIPTION 🫶

so gmx spol looks at the dipoles hanging around a solute, and it is especially that girl for polarizable water 💧. To even start, you need two things: a group of reference atoms — or a center of mass reference if you flip the -com option on — and a group of solvent atoms. That's it, that's the entry fee 🎟️.

Then the program gets to work: it splits that group of solvent atoms into molecules 🧚✨. For every solvent molecule, it works out the distance to the closest atom in the reference group, or to the COM if you went the COM route. Then it plots a cumulative distribution of all those distances 📈.

For each distance that falls between -rmin and -rmax, it determines the inner product of the distance vector and the dipole of the solvent molecule. And here's a lil detail that matters: for solvent molecules with net charge (i.e. ions 👀), the net charge of the ion gets subtracted evenly from all atoms in the selection of each ion. Then the average of these dipole components is printed 🖨️.

The exact same glow-up happens for the polarization, except there the average dipole is subtracted from the instantaneous dipole. The magnitude of the average dipole is set with the -dip option, and the direction is defined by the vector from the first atom in the selected solvent group to the midpoint between the second and the third atom 🎯.

✨ OPTIONS ✨

📥 Options to specify input files:

  • -f [<.xtc/.trr/...>] (traj.xtc) — the trajectory file, and it takes: xtc trr cpt gro g96 pdb tng h5md 🎞️
  • -s [<.tpr>] (topol.tpr) — a Portable xdr run input file, aka the standard GROMACS .tpr bestie
  • -n [<.ndx>] (index.ndx) (Optional) — an index file, totally optional, only if you want it 💅

📤 Options to specify output files:

  • -o [<.xvg>] (scdist.xvg) — the output, an xvgr/xmgr file 📊

🎀 Other options:

  • -b <time> (0) — the time of the first frame to read from the trajectory (default unit: ps) ⏰
  • -e <time> (0) — the time of the last frame to read from the trajectory (default unit: ps) ⏳
  • -dt <time> (0) — only use a frame when t MOD dt = first time (default unit: ps) 🔂
  • -[no]w (no) — view the output .xvg, .xpm, .eps and .pdb files, cute little preview moment 👀
  • -xvg <enum> (xmgrace) — xvg plot formatting, pick your fighter: xmgrace, xmgr, none 🎨
  • -[no]com (no) — use the center of mass as the reference position 🎯
  • -refat <int> (1) — the reference atom of the solvent molecule 🔬
  • -rmin <real> (0) — Maximum distance (nm) 📏
  • -rmax <real> (0.32) — Maximum distance (nm) 📏
  • -dip <real> (0) — the average dipole (D) ⚡
  • -bw <real> (0.01) — the bin width 🗂️

👑 SEE ALSO 👑

2026, GROMACS development team

okay and that's the whole page bestie 🫶 this was GROMACS 2026.4, dated Oct 02, 2026, and the manpage you just read is GMX-SPOL(1). slay, go analyze some dipoles, ily, drink water 💖🦋✨

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