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GMX-MSD(1) GROMACS GMX-MSD(1) NAME gmx-msd - Compute mean squared displacements SYNOPSIS gmx msd [-f [<.xtc/.trr/...>]] [-s [<.tpr/.gro/...>]] [-n [<.ndx>]] [-o [<.xvg>]] [-mol [<.xvg>]] [-b <time>] [-e <time>] [-dt <time>] [-tu <enum>] [-fgroup <selection>] [-xvg <enum>] [-[no]rmpbc] [-[no]pbc] [-sf <file>] [-selrpos <enum>] [-seltype <enum>] [-sel <selection>] [-type <enum>] [-lateral <enum>] [-trestart <real>] [-maxtau <real>] [-beginfit <real>] [-endfit <real>] DESCRIPTION gmx msd computes the mean square displacement (MSD) of atoms from a set of initial positions. This provides an easy way to compute the diffu- sion constant using the Einstein relation. The time between the refer- ence points for the MSD calculation is set with -trestart. The diffu- sion constant is calculated by least squares fitting a straight line (D*t + c) through the MSD(t) from -beginfit to -endfit (note that t is time from the reference positions, not simulation time). An error esti- mate given, which is the difference of the diffusion coefficients ob- tained from fits over the two halves of the fit interval. There are three, mutually exclusive, options to determine different types of mean square displacement: -type, -lateral and -ten. Option -ten writes the full MSD tensor for each group, the order in the output is: trace xx yy zz yx zx zy. If -mol is set, gmx msd plots the MSD for individual molecules (includ- ing making molecules whole across periodic boundaries): for each indi- vidual molecule a diffusion constant is computed for its center of mass. The chosen index group will be split into molecules. With -mol, only one index group can be selected. The diffusion coefficient is determined by linear regression of the MSD. When -beginfit is -1, fitting starts at 10% and when -endfit is -1, fitting goes to 90%. Using this option one also gets an accurate error estimate based on the statistics between individual molecules. Note that this diffusion coefficient and error estimate are only accu- rate when the MSD is completely linear between -beginfit and -endfit. By default, gmx msd compares all trajectory frames against every frame stored at -trestart intervals, so the number of frames stored scales linearly with the number of frames processed. This can lead to long analysis times and out-of-memory errors for long/large trajectories, and often the data at higher time deltas lacks sufficient sampling, of- ten manifesting as a wobbly line on the MSD plot after a straighter re- gion at lower time deltas. The -maxtau option can be used to cap the maximum time delta for frame comparison, which may improve performance and can be used to avoid out-of-memory issues. OPTIONS Options to specify input files: -f [<.xtc/.trr/...>] (traj.xtc) (Optional) Input trajectory or single configuration: xtc trr cpt gro g96 pdb tng -s [<.tpr/.gro/...>] (topol.tpr) (Optional) Input structure: tpr gro g96 pdb brk ent -n [<.ndx>] (index.ndx) (Optional) Extra index groups Options to specify output files: -o [<.xvg>] (msdout.xvg) (Optional) MSD output -mol [<.xvg>] (diff_mol.xvg) (Optional) Report diffusion coefficients for each molecule in selection Other options: -b <time> (0) First frame (ps) to read from trajectory -e <time> (0) Last frame (ps) to read from trajectory -dt <time> (0) Only use frame if t MOD dt == first time (ps) -tu <enum> (ps) Unit for time values: fs, ps, ns, us, ms, s -fgroup <selection> Atoms stored in the trajectory file (if not set, assume first N atoms) -xvg <enum> (xmgrace) Plot formatting: xmgrace, xmgr, none -[no]rmpbc (yes) Make molecules whole for each frame -[no]pbc (yes) Use periodic boundary conditions for distance calculation -sf <file> Provide selections from files -selrpos <enum> (atom) Selection reference positions: atom, res_com, res_cog, mol_com, mol_cog, whole_res_com, whole_res_cog, whole_mol_com, whole_mol_cog, part_res_com, part_res_cog, part_mol_com, part_mol_cog, dyn_res_com, dyn_res_cog, dyn_mol_com, dyn_mol_cog -seltype <enum> (atom) Default selection output positions: atom, res_com, res_cog, mol_com, mol_cog, whole_res_com, whole_res_cog, whole_mol_com, whole_mol_cog, part_res_com, part_res_cog, part_mol_com, part_mol_cog, dyn_res_com, dyn_res_cog, dyn_mol_com, dyn_mol_cog -sel <selection> Selections to compute MSDs for from the reference -type <enum> (unused) : x, y, z, unused -lateral <enum> (unused) : x, y, z, unused -trestart <real> (10) Time between restarting points in trajectory (ps) -maxtau <real> (1.79769e+308) Maximum time delta between frames to calculate MSDs for (ps) -beginfit <real> (-1) Time point at which to start fitting. -endfit <real> (-1) End time for fitting. SEE ALSO gmx(1) More information about GROMACS is available at <- http://www.gromacs.org/>. COPYRIGHT 2025, GROMACS development team 2025.0 Feb 10, 2025 GMX-MSD(1)
NAME | SYNOPSIS | DESCRIPTION | OPTIONS | SEE ALSO | COPYRIGHT
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