分析梳理--分子动力学模拟的常规步骤七（Gromacs）

title = OPLS Lysozyme NPT Production

; Run parameters
integrator = md
nsteps = 50000          ; 100 ps（生产跑通常更长，按需调整）
dt = 0.002

; Output control（关键：必须指定 xtc 输出）
nstxout             = 0     ; 不输出未压缩坐标
nstvout             = 0     
nstfout             = 0
nstxout-compressed  = 5000  ; ✅ 每 5000 步写一次 .xtc（生成轨迹）
nstenergy           = 5000
nstlog              = 5000

; Bond parameters
continuation        = yes   ; ⚠️ 生产跑：从已有速度继续
constraint_algorithm = lincs
constraints         = all-bonds
lincs_iter          = 1
lincs_order         = 4

; Neighbor searching / electrostatics（建议补齐，避免用默认值）
cutoff-scheme       = Verlet
ns_type             = grid
rlist               = 1.0
coulombtype         = PME
rcoulomb            = 1.0
vdwtype             = Cut-off
rvdw                = 1.0

; Temperature coupling
tcoupl              = V-rescale
tc-grps             = Protein Non-Protein
tau_t               = 0.1   0.1
ref_t               = 300   300

; Pressure coupling（保持不变，说明你确实要跑 NPT）
pcoupl              = Parrinello-Rahman
pcoupltype          = isotropic
tau_p               = 2.0
ref_p               = 1.0
compressibility     = 4.5e-5
refcoord_scaling    = com

; PBC & dispersion
pbc                 = xyz
DispCorr            = EnerPres

; Velocity generation（生产跑：不从零生成速度）
gen_vel             = no

gmx trjconv -s md_0_I.tpr -f md.xtc -o md_0_I_noPBC.xtc -pbc mol -ur compact

Options to specify input files:

 -f      [<.xtc/.trr/...>]  (traj.xtc)
           Trajectory: xtc trr cpt gro g96 pdb tng
 -s      [<.tpr/.gro/...>]  (topol.tpr)      (Opt.)
           Structure+mass(db): tpr gro g96 pdb brk ent
 -n      [<.ndx>]           (index.ndx)      (Opt.)
           Index file
 -fr     [<.ndx>]           (frames.ndx)     (Opt.)
           Index file
 -sub    [<.ndx>]           (cluster.ndx)    (Opt.)
           Index file
 -drop   [<.xvg>]           (drop.xvg)       (Opt.)
           xvgr/xmgr file

Options to specify output files:

 -o      [<.xtc/.trr/...>]  (trajout.xtc)
           Trajectory: xtc trr gro g96 pdb tng

Other options:

 -b      <time>             (0)
           Time of first frame to read from trajectory (default unit ps)
 -e      <time>             (0)
           Time of last frame to read from trajectory (default unit ps)
 -tu     <enum>             (ps)
           Unit for time values: fs, ps, ns, us, ms, s
 -[no]w                     (no)
           View output .xvg, .xpm, .eps and .pdb files
 -xvg    <enum>             (xmgrace)
           xvg plot formatting: xmgrace, xmgr, none
 -skip   <int>              (1)
           Only write every nr-th frame
 -dt     <time>             (0)
           Only write frame when t MOD dt = first time (ps)
 -[no]round                 (no)
           Round measurements to nearest picosecond
 -dump   <time>             (-1)
           Dump frame nearest specified time (ps)
 -t0     <time>             (0)
           Starting time (ps) (default: don't change)
 -timestep <time>           (0)
           Change time step between input frames (ps)
 -pbc    <enum>             (none)
           PBC treatment (see help text for full description): none, mol, res,
           atom, nojump, cluster, whole
 -ur     <enum>             (rect)
           Unit-cell representation: rect, tric, compact
 -[no]center                (no)
           Center atoms in box
 -boxcenter <enum>          (tric)
           Center for -pbc and -center: tric, rect, zero
 -box    <vector>           (0 0 0)
           Size for new cubic box (default: read from input)
 -trans  <vector>           (0 0 0)
           All coordinates will be translated by trans. This can
           advantageously be combined with -pbc mol -ur compact.
 -shift  <vector>           (0 0 0)
           All coordinates will be shifted by framenr*shift
 -fit    <enum>             (none)
           Fit molecule to ref structure in the structure file: none,
           rot+trans, rotxy+transxy, translation, transxy, progressive
 -ndec   <int>              (3)
           Number of decimal places to write to .xtc output
 -[no]vel                   (yes)
           Read and write velocities if possible
 -[no]force                 (no)
           Read and write forces if possible
 -trunc  <time>             (-1)
           Truncate input trajectory file after this time (ps)
 -exec   <string>
           Execute command for every output frame with the frame number as
           argument
 -split  <time>             (0)
           Start writing new file when t MOD split = first time (ps)
 -[no]sep                   (no)
           Write each frame to a separate .gro, .g96 or .pdb file
 -nzero  <int>              (0)
           If the -sep flag is set, use these many digits for the file numbers
           and prepend zeros as needed
 -dropunder <real>          (0)
           Drop all frames below this value
 -dropover <real>           (0)
           Drop all frames above this value
 -[no]conect                (no)
           Add CONECT PDB records when writing .pdb files. Useful for
           visualization of non-standard molecules, e.g. coarse grained ones.
           Can only be done when a topology (tpr) file is present

gmx rms -s md_0_I.tpr -f md_0_I_noPBC.xtc -o rmsd.xvg -tu ns

gmx rms -s em.tpr -f md_0_I_noPBC.xtc -o rmsd_xtal.xvg -tu ns

Options to specify input files:

 -s      [<.tpr/.gro/...>]  (topol.tpr)
           Structure+mass(db): tpr gro g96 pdb brk ent
 -f      [<.xtc/.trr/...>]  (traj.xtc)
           Trajectory: xtc trr cpt gro g96 pdb tng
 -f2     [<.xtc/.trr/...>]  (traj.xtc)       (Opt.)
           Trajectory: xtc trr cpt gro g96 pdb tng
 -n      [<.ndx>]           (index.ndx)      (Opt.)
           Index file

Options to specify output files:

 -o      [<.xvg>]           (rmsd.xvg)
           xvgr/xmgr file
 -mir    [<.xvg>]           (rmsdmir.xvg)    (Opt.)
           xvgr/xmgr file
 -a      [<.xvg>]           (avgrp.xvg)      (Opt.)
           xvgr/xmgr file
 -dist   [<.xvg>]           (rmsd-dist.xvg)  (Opt.)
           xvgr/xmgr file
 -m      [<.xpm>]           (rmsd.xpm)       (Opt.)
           X PixMap compatible matrix file
 -bin    [<.dat>]           (rmsd.dat)       (Opt.)
           Generic data file
 -bm     [<.xpm>]           (bond.xpm)       (Opt.)
           X PixMap compatible matrix file

Other options:

 -b      <time>             (0)
           Time of first frame to read from trajectory (default unit ps)
 -e      <time>             (0)
           Time of last frame to read from trajectory (default unit ps)
 -dt     <time>             (0)
           Only use frame when t MOD dt = first time (default unit ps)
 -tu     <enum>             (ps)
           Unit for time values: fs, ps, ns, us, ms, s
 -[no]w                     (no)
           View output .xvg, .xpm, .eps and .pdb files
 -xvg    <enum>             (xmgrace)
           xvg plot formatting: xmgrace, xmgr, none
 -what   <enum>             (rmsd)
           Structural difference measure: rmsd, rho, rhosc
 -[no]pbc                   (yes)
           PBC check
 -fit    <enum>             (rot+trans)
           Fit to reference structure: rot+trans, translation, none
 -prev   <int>              (0)
           Compare with previous frame
 -[no]split                 (no)
           Split graph where time is zero
 -skip   <int>              (1)
           Only write every nr-th frame to matrix
 -skip2  <int>              (1)
           Only write every nr-th frame to matrix
 -max    <real>             (-1)
           Maximum level in comparison matrix
 -min    <real>             (-1)
           Minimum level in comparison matrix
 -bmax   <real>             (-1)
           Maximum level in bond angle matrix
 -bmin   <real>             (-1)
           Minimum level in bond angle matrix
 -[no]mw                    (yes)
           Use mass weighting for superposition
 -nlevels <int>             (80)
           Number of levels in the matrices
 -ng     <int>              (1)
           Number of groups to compute RMS between