为了方便使用可视化软件查看模拟的结果，经常需要将结果合并成pdb等文件，然后用shell远程下载文件后查看。
用trjconv 命令合并生产文件，-s 输入tpr能量文件，-f 输入xtc文件，最后-o表示输出文件。-pbc 后面的
是表示读取里面的数据，后面需要选择，命令如下：
trjconv -s dppc-md.tpr -f dppc-md.xtc -o dppc-md.pdb -pbc whole -conect
:-) trjconv (-:
Option Filename Type Description
------------------------------------------------------------
-f dynamic.xtc Input Trajectory: xtc trr trj gro g96 pdb cpt
-o dynamic.pdb Output Trajectory: xtc trr trj gro g96 pdb
-s dynamic.tpr Input, Opt! Structure+mass(db): tpr tpb tpa gro g96 pdb
-n index.ndx Input, Opt. Index file
-fr frames.ndx Input, Opt. Index file
-sub cluster.ndx Input, Opt. Index file
-drop drop.xvg Input, Opt. xvgr/xmgr file
Option Type Value Description
------------------------------------------------------
-[no]h bool no Print help info and quit
-[no]version bool no Print version info and quit
-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 or s
-[no]w bool no View output .xvg, .xpm, .eps and .pdb files
-xvg enum xmgrace xvg plot formatting: xmgrace, xmgr or 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 bool 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 whole PBC treatment (see help text for full
description): none, mol, res, atom, nojump,
cluster or whole
-ur enum rect Unit-cell representation: rect, tric or compact
-[no]center bool no Center atoms in box
-boxcenter enum tric Center for -pbc and -center: tric, rect or zero
-box vector 0 0 0 Size for new cubic box (default: read from input)
-clustercenter vector 0 0 0 Optional starting point for pbc cluster option
-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 or progressive
-ndec int 3 Precision for .xtc and .gro writing in number of
decimal places
-[no]vel bool yes Read and write velocities if possible
-[no]force bool 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
-[no]app bool no Append output
-split time 0 Start writing new file when t MOD split = first
time (ps)
-[no]sep bool 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 bool yes Add conect records when writing .pdb files.
Useful for visualization of non-standard
molecules, e.g. coarse grained ones
And the next is to choose which part you want to fill :
Reading file dynamic.tpr, VERSION 4.6.5 (single precision)
Select group for output
Group 0 ( System) has 906 elements
Group 1 ( Protein) has 163 elements
Group 2 ( Protein-H) has 163 elements
Group 3 ( C-alpha) has 0 elements
Group 4 ( Backbone) has 0 elements
Group 5 ( MainChain) has 0 elements
Group 6 ( MainChain+Cb) has 0 elements
Group 7 ( MainChain+H) has 0 elements
Group 8 ( SideChain) has 163 elements
Group 9 ( SideChain-H) has 163 elements
Group 10 ( Prot-Masses) has 163 elements
Group 11 ( non-Protein) has 743 elements
Group 12 ( Other) has 743 elements
Group 13 ( W) has 743 elements
Select a group:
Choose "System" mean everything of this design.
可以根据自己的需要进行选择生成。0代表系统里面的全部都转换。