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gmx trjconv 保持分子完整性,pbc周期边界设置

作者:小宝 2017-05-31 19:05:54

在模拟完成后经常因为分子超出边界而导致分子不完整,那么gmx trjconv可以保持分子的完整性。

gmx trjconv也可以将模拟补数设置为ns,fs,ms等时间单位,方便观察。运行gmx trjconv -h可以查看相关设置。

用法:gmx trjconv -f product.xtc -o pbc-ns.xtc  -tu ns  -pbc whole 

上面将我模拟后的轨迹用ns表示,并且保持分子的完整性,输出为pbc-ns.xtc

这个命令还有很多设置,常用的是是pbc和tu参数。下面是运行帮助的结果,可以看出有很多功能。

Options to specify input and output files:

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

Other options:

 -nice  <int>    (19)       Set the nicelevel
 -b     <time>   (0)        First frame (ps) to read from trajectory
 -e     <time>   (0)        Last frame (ps) to read from trajectory
 -tu    <enum>   (ps)       Time unit: 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)
     Precision for .xtc and .gro writing in number of decimal places
 -[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 records when writing .pdb files. Useful for visualization of
     non-standard molecules, e.g. coarse grained ones

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