分子动力学模拟套件
简介
gmx [-[no]h] [-[no]quiet] [-[no]version] [-[no]copyright] [-nice <int>]
[-[no]backup]描述
GROMACS是一套功能齐全的程序，用于执行分子动力学模拟，即使用牛顿运动方程模拟具有数亿到数百万个粒子的系统的行为。它主要用于蛋白质、脂质和聚合物的研究，但也可应用于各种化学和生物研究问题。
选项
-[no]h (no)
Print help and quit
-[no]quiet (no)
Do not print common startup info or quotes
-[no]version (no)
Print extended version information and quit
-[no]copyright (no)
Print copyright information on startup
-nice <int> (19)
Set the nicelevel (default depends on command)
-[no]backup (yes)
Write backups if output files existgmx 命令
以下命令可用。请参阅对应的gmx帮助页<command>了解更多详细信息。
轨迹分析
gmx-gangle(1) Calculate angles
gmx-convert-trj(1) Converts between different trajectory types
gmx-distance(1) Calculate distances between pairs of positions
gmx-dssp(1) Calculate protein secondary structure via DSSP algorithm
gmx-extract-cluster(1) Allows extracting frames corresponding to clusters from trajectory
gmx-freevolume(1) Calculate free volume
gmx-hbond(1) Compute and analyze hydrogen bonds.
gmx-msd(1) Compute mean squared displacements
gmx-pairdist(1) Calculate pairwise distances between groups of positions
gmx-rdf(1) Calculate radial distribution functions
gmx-sasa(1) Compute solvent accessible surface area
gmx-scattering(1) Calculate small angle scattering profiles for SANS or SAXS
gmx-select(1) Print general information about selections
gmx-trajectory(1) Print coordinates, velocities, and/or forces for selections
gmx-gyrate(1) Calculate radius of gyration of a molecule
生成拓扑和坐标
gmx-editconf(1) Edit the box and write subgroups
gmx-x2top(1) Generate a primitive topology from coordinates
gmx-solvate(1) Solvate a system
gmx-insert-molecules(1) Insert molecules into existing vacancies
gmx-genconf(1) Multiply a conformation in ‘random’ orientations
gmx-genion(1) Generate monoatomic ions on energetically favorable positions
gmx-genrestr(1) Generate position restraints or distance restraints for index groups
gmx-pdb2gmx(1) Convert coordinate files to topology and FF-compliant coordinate files
运行模拟
gmx-grompp(1) Make a run input file
gmx-mdrun(1) Perform a simulation, do a normal mode analysis or an energy minimization
gmx-convert-tpr(1) Make a modified run-input file
查看轨迹
gmx-nmtraj(1) Generate a virtual oscillating trajectory from an eigenvector
处理能量
gmx-enemat(1) Extract an energy matrix from an energy file
gmx-energy(1) Writes energies to xvg files and display averages
gmx-mdrun(1) (Re)calculate energies for trajectory frames with -rerun
转换文件格式
gmx-editconf(1) Convert and manipulates structure files
gmx-eneconv(1) Convert energy files
gmx-sigeps(1) Convert c6/12 or c6/cn combinations to and from sigma/epsilon
gmx-trjcat(1) Concatenate trajectory files
gmx-trjconv(1) Convert and manipulates trajectory files
gmx-xpm2ps(1) Convert XPM (XPixelMap) matrices to postscript or XPM
工具
gmx-analyze(1) Analyze data sets
gmx-awh(1) Extract data from an accelerated weight histogram (AWH) run
gmx-filter(1) Frequency filter trajectories, useful for making smooth movies
gmx-lie(1) Estimate free energy from linear combinations
gmx-pme_error(1) Estimate the error of using PME with a given input file
gmx-sham(1) Compute free energies or other histograms from histograms
gmx-spatial(1) Calculate the spatial distribution function
gmx-traj(1) Plot x, v, f, box, temperature and rotational energy from trajectories
gmx-tune_pme(1) Time mdrun as a function of PME ranks to optimize settings
gmx-wham(1) Perform weighted histogram analysis after umbrella sampling
gmx-check(1) Check and compare files
gmx-dump(1) Make binary files human readable
gmx-make_ndx(1) Make index files
gmx-mk_angndx(1) Generate index files for ‘gmx angle’
gmx-trjorder(1) Order molecules according to their distance to a group
gmx-xpm2ps(1) Convert XPM (XPixelMap) matrices to postscript or XPM
gmx-report-methods(1) Write short summary about the simulation setup to a text file and/or to the standard output.
计算结构距离
gmx-cluster(1) Cluster structures
gmx-confrms(1) Fit two structures and calculates the RMSD
gmx-rms(1) Calculate RMSDs with a reference structure and RMSD matrices
gmx-rmsf(1) Calculate atomic fluctuations
计算结构距离随时间的变化
gmx-mindist(1) Calculate the minimum distance between two groups
gmx-mdmat(1) Calculate residue contact maps
gmx-polystat(1) Calculate static properties of polymers
gmx-rmsdist(1) Calculate atom pair distances averaged with power -2, -3 or -6
随时间变化的质量分布特性
gmx-gyrate-legacy(1) Calculate the radius of gyration
gmx-polystat(1) Calculate static properties of polymers
gmx-rdf(1) Calculate radial distribution functions
gmx-rotacf(1) Calculate the rotational correlation function for molecules
gmx-rotmat(1) Plot the rotation matrix for fitting to a reference structure
gmx-sans-legacy(1) Compute small angle neutron scattering spectra
gmx-saxs-legacy(1) Compute small angle X-ray scattering spectra
gmx-traj(1) Plot x, v, f, box, temperature and rotational energy from trajectories
gmx-vanhove(1) Compute Van Hove displacement and correlation functions
分析绑定交互
gmx-angle(1) Calculate distributions and correlations for angles and dihedrals
gmx-mk_angndx(1) Generate index files for ‘gmx angle’
结构特性
gmx-bundle(1) Analyze bundles of axes, e.g., helices
gmx-clustsize(1) Calculate size distributions of atomic clusters
gmx-disre(1) Analyze distance restraints
gmx-hbond-legacy(1) Compute and analyze hydrogen bonds
gmx-order(1) Compute the order parameter per atom for carbon tails
gmx-principal(1) Calculate principal axes of inertia for a group of atoms
gmx-rdf(1) Calculate radial distribution functions
gmx-saltbr(1) Compute salt bridges
gmx-sorient(1) Analyze solvent orientation around solutes
gmx-spol(1) Analyze solvent dipole orientation and polarization around solutes
动力学特性
gmx-bar(1) Calculate free energy difference estimates through Bennett’s acceptance ratio
gmx-current(1) Calculate dielectric constants and current autocorrelation function
gmx-dos(1) Analyze density of states and properties based on that
gmx-dyecoupl(1) Extract dye dynamics from trajectories
gmx-principal(1) Calculate principal axes of inertia for a group of atoms
gmx-tcaf(1) Calculate viscosities of liquids
gmx-traj(1) Plot x, v, f, box, temperature and rotational energy from trajectories
gmx-vanhove(1) Compute Van Hove displacement and correlation functions
gmx-velacc(1) Calculate velocity autocorrelation functions
静电特性
gmx-current(1) Calculate dielectric constants and current autocorrelation function
gmx-dielectric(1) Calculate frequency dependent dielectric constants
gmx-dipoles(1) Compute the total dipole plus fluctuations
gmx-potential(1) Calculate the electrostatic potential across the box
gmx-spol(1) Analyze solvent dipole orientation and polarization around solutes
gmx-genion(1) Generate monoatomic ions on energetically favorable positions
蛋白质特异性分析
gmx-chi(1) Calculate everything you want to know about chi and other dihedrals
gmx-helix(1) Calculate basic properties of alpha helices
gmx-helixorient(1) Calculate local pitch/bending/rotation/orientation inside helices
gmx-rama(1) Compute Ramachandran plots
gmx-wheel(1) Plot helical wheels
接口
gmx-bundle(1) Analyze bundles of axes, e.g., helices
gmx-density(1) Calculate the density of the system
gmx-densmap(1) Calculate 2D planar or axial-radial density maps
gmx-densorder(1) Calculate surface fluctuations
gmx-h2order(1) Compute the orientation of water molecules
gmx-hydorder(1) Compute tetrahedrality parameters around a given atom
gmx-order(1) Compute the order parameter per atom for carbon tails
gmx-potential(1) Calculate the electrostatic potential across the box
协方差分析
gmx-anaeig(1) Analyze the eigenvectors
gmx-covar(1) Calculate and diagonalize the covariance matrix
gmx-make_edi(1) Generate input files for essential dynamics sampling
正常模式
gmx-anaeig(1) Analyze the normal modes
gmx-nmeig(1) Diagonalize the Hessian for normal mode analysis
gmx-nmtraj(1) Generate a virtual oscillating trajectory from an eigenvector
gmx-nmens(1) Generate an ensemble of structures from the normal modes
gmx-grompp(1) Make a run input file
gmx-mdrun(1) Find a potential energy minimum and calculate the Hessian