gmx rms rmsf rmsdist
總結(jié)
gmx rms -f *.xtc -s *.tpr -o *_rmsd.xvg -m *_rmsd.xpm -tu ns
gmx rmsf -f *.xtc -s *.tpr -oq *_bfactor.pdb(默認(rèn)寫(xiě)到-s文件中，或者用-q提供一個(gè)新的pdb寫(xiě)入bfactor) -o *_rmsf.xvg -res(一定要加，否則算的是atom的)
幾個(gè)概念：rmsd vs rmsf vs rmsdist
RMSD 是對(duì)原子總數(shù)求平均， RMSF 是對(duì)單個(gè)原子時(shí)間求平均
RMSD表示的是分子結(jié)構(gòu)變化的程度，而RMSF值表示的是分子中各個(gè)原子運(yùn)動(dòng)的自由程度
rmsd
計(jì)算的是某個(gè)結(jié)構(gòu)（N個(gè)原子）相對(duì)于參考結(jié)構(gòu)（-s指定）的 root mean square deviation
rmsf
計(jì)算的是一個(gè)原子在一段時(shí)間的平均，和bfactor有關(guān)
rmsdist 計(jì)算的是原子i和j直接的距離隨時(shí)間的變化大小，rmsd算的是原子i相對(duì)自己的位置變化大小
OPTIONS
Options to specify input files:
-s [<.tpr/.gro/...>] (topol.tpr) //參考結(jié)構(gòu)reference structure
Structure+mass(db): tpr gro g96 pdb brk ent
The reference structure is taken from the structure file (-s).
-f [<.xtc/.trr/...>] (traj.xtc)
Trajectory: xtc trr cpt gro g96 pdb tng
Each structure from a trajectory (-f) is compared to a reference structure.
-f2 [<.xtc/.trr/...>] (traj.xtc) (Opt.) //算矩陣的時(shí)候，默認(rèn)是第一個(gè)trj和第一個(gè)trj每一幀計(jì)算rmsd，用-f2則是第一個(gè)trj和第二個(gè)trj每一幀比較rmsd
Trajectory: xtc trr cpt gro g96 pdb tng
With -f2, the 'other structures' are taken from a second trajectory, this generates a comparison matrix of one trajectory versus the other.
-n [<.ndx>] (index.ndx) (Opt.)
Index file
Options to specify output files:
-o [<.xvg>] (rmsd.xvg)
xvgr/xmgr file
-mir [<.xvg>] (rmsdmir.xvg) (Opt.) // the mirror image of the reference structure 不需要
xvgr/xmgr file
With option -mir also a comparison with the mirror image of the reference structure is calculated. This is useful as a reference for 'significant' values, see Maiorov & Crippen, Proteins 22, 273 (1995).
-a [<.xvg>] (avgrp.xvg) (Opt.) 不需要
xvgr/xmgr file
-dist [<.xvg>] (rmsd-dist.xvg) (Opt.) 不需要
xvgr/xmgr file
-m [<.xpm>] (rmsd.xpm) (Opt.)
X PixMap compatible matrix file
Option -m produces a matrix in .xpm format of comparison values of each structure in the trajectory with respect to each other structure . This file can be visualized with for instance xv and can be converted to postscript with gmx xpm2ps.
-bin [<.dat>] (rmsd.dat) (Opt.)
Generic data file
Option -bin does a binary dump of the comparison matrix .
-bm [<.xpm>] (bond.xpm) (Opt.) //角度的矩陣
X PixMap compatible matrix file
Option -bm produces a matrix of average bond angle deviations analogously to the -m option. Only bonds between atoms in the comparison group are considered.
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
gmx rms compares two structures by computing the root mean square deviation (RMSD), the size-independent rho similarity parameter (rho) or the scaled rho (rhosc), see Maiorov & Crippen, Proteins 22, 273 (1995). This is selected by -what
-[no]pbc (yes)
PBC check
-fit <enum> (rot+trans) //默認(rèn)rot+trans，不需要
Fit to reference structure: rot+trans, translation, none
Option -fit controls the least-squares fitting of the structures on top of each other: complete fit (rotation and translation), translation only, or no fitting at all.
-prev <int> (0) //而不是ref
Compare with previous frame
Option -prev produces the comparison with a previous frame the specified number of frames ago.
-[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) 不需要
Use mass weighting for superposition
Option -mw controls whether mass weighting is done or not. If you select the option (default) and supply a valid .tpr file masses will be taken from there, otherwise the masses will be deduced from the atommass.dat file in GMXLIB. This is fine for proteins, but not necessarily for other molecules. A default mass of 12.011 amu (carbon) is assigned to unknown atoms. You can check whether this happened by turning on the -debug flag and inspecting the log file.
-nlevels <int> (80) //xpm為的z分80個(gè)level,不需要改
Number of levels in the matrices
-ng <int> (1) //意思可能是可以算兩個(gè)grp的rms
Number of groups to compute RMS between
OPTIONS
Options to specify input files:
-f [<.xtc/.trr/...>] (traj.xtc)
Trajectory: xtc trr cpt gro g96 pdb tng
-s [<.tpr/.gro/...>] (topol.tpr) // a reference frame
Structure+mass(db): tpr gro g96 pdb brk ent
gmx rmsf computes the root mean square fluctuation (RMSF, i.e. standard deviation) of atomic positions in the trajectory (supplied with -f) after (optionally) fitting to a reference frame (supplied with -s).
-n [<.ndx>] (index.ndx) (Opt.)
Index file
-q [<.pdb>] (eiwit.pdb) (Opt.)
Protein data bank file
Options to specify output files:
-oq [<.pdb>] (bfac.pdb) (Opt.) //計(jì)算并保存B-factor values到-s提供的結(jié)構(gòu)中 或者 可以用-q提供一個(gè)新的pdb結(jié)構(gòu)
Protein data bank file
With option -oq the RMSF values are converted to B-factor values, which are written to a .pdb file. By default, the coordinates in this output file are taken from the structure file provided with -s,although you can also use coordinates read from a different .pdb file provided with -q. There is very little error checking, so in this caseit is your responsibility to make sure all atoms in the structure file and .pdb file correspond exactly to each other.
-ox [<.pdb>] (xaver.pdb) (Opt.) //計(jì)算并保存B-factor values到平均結(jié)構(gòu)中
Protein data bank file
Option -ox writes the B-factors to a file with the average coordinates in the trajectory.
-o [<.xvg>] (rmsf.xvg)
xvgr/xmgr file
-od [<.xvg>] (rmsdev.xvg) (Opt.) //和rmsf算出來(lái)的一樣，沒(méi)用
xvgr/xmgr file
With the option -od the root mean square deviation with respect to the reference structure is calculated.
-oc [<.xvg>] (correl.xvg) (Opt.)
xvgr/xmgr file
-dir [<.log>] (rmsf.log) (Opt.)
Log file
With option -dir the average MSF (3x3) matrix is diagonalized. This shows the directions in which the atoms fluctuate the most and the least.
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)
-[no]w (no)
View output .xvg, .xpm, .eps and .pdb files
-xvg <enum> (xmgrace)
xvg plot formatting: xmgrace, xmgr, none
-[no]res (no) //一定要
Calculate averages for each residue
-[no]aniso (no) //各向異性溫度因子
Compute anisotropic termperature factors
With the option -aniso, gmx rmsf will compute anisotropic temperature factors and then it will also output average coordinates and a .pdb file with ANISOU records (corresonding to the -oq or -ox option). Please note that the U values are orientation-dependent, so before comparison with experimental data you should verify that you fit to the experimental coordinates. When a .pdb input file is passed to the program and the -aniso flag is set a correlation plot of the Uij will be created, if any anisotropic temperature factors are present in the .pdb file.
使用-aniso選項(xiàng)，gmx rmsf將計(jì)算各向異性溫度因子，然后它還將輸出平均坐標(biāo)和帶有ANISOU記錄的.pdb文件(與-oq或-ox選項(xiàng)相對(duì)應(yīng))。請(qǐng)注意U值是與方向相關(guān)的，因此在與實(shí)驗(yàn)數(shù)據(jù)進(jìn)行比較之前，您應(yīng)該驗(yàn)證您是否適合實(shí)驗(yàn)坐標(biāo)。當(dāng)將.pdb輸入文件傳遞給程序并設(shè)置-aniso標(biāo)志時(shí)，如果.pdb文件中存在任何各向異性溫度因子，則會(huì)創(chuàng)建Uij的相關(guān)圖。
-[no]fit (yes)
Do a least squares superposition before computing RMSF. Without this you must make sure that the reference structure and the trajectory match.
computes the root mean square deviation of atom distances , which has the advantage that no fit is needed like in standard RMS deviation as computed by gmx rms. The reference structure is taken from the structure file.
The RMSD at time t is calculated as the RMS of the differences in distance between atom-pairs in the reference structure and the structure at time t.
gmx rmsdist can also produce matrices of the rms distances , rms distances scaled with the mean distance and the mean distances and matrices with NMR averaged distances (1/r^3 and 1/r^6 averaging). Finally, lists of atom pairs with 1/r^3 and 1/r^6 averaged distance below the maximum distance (-max, which will default to 0.6 in this case) can be generated, by default averaging over equivalent hydrogens (all triplets of hydrogens named *[123]).
OPTIONS
Options to specify input files:
-f [<.xtc/.trr/...>] (traj.xtc)
Trajectory: xtc trr cpt gro g96 pdb tng
-s [<.tpr/.gro/...>] (topol.tpr)
Structure+mass(db): tpr gro g96 pdb brk ent
-n [<.ndx>] (index.ndx) (Opt.)
Index file
-equiv [<.dat>] (equiv.dat) (Opt.)
Generic data file
Additionally a list of equivalent atoms can be supplied ( -equiv), each line containing a set of equivalent atoms specified as residue number and name and atom name;
e.g.: HB* 3 SER HB1 3 SER HB2. //可能第一列要給距離命名
Residue and atom names must exactly match those in the structure file, including case. Specifying non-sequential atoms is undefined.
此外，還可以提供等效原子列表(-equiv)，每行包含一組等效原子，這些原子指定為殘基編號(hào)和名稱以及原子名稱;例如:HB* 3 SER HB1 3 SER HB2。殘基編號(hào)和原子名稱必須與結(jié)構(gòu)文件中的名稱完全匹配，包括case。未定義指定非順序原子。
Options to specify output files:
-o [<.xvg>] (distrmsd.xvg)
xvgr/xmgr file
-rms [<.xpm>] (rmsdist.xpm) (Opt.)
X PixMap compatible matrix file
-scl [<.xpm>] (rmsscale.xpm) (Opt.)
X PixMap compatible matrix file
-mean [<.xpm>] (rmsmean.xpm) (Opt.)
X PixMap compatible matrix file
-nmr3 [<.xpm>] (nmr3.xpm) (Opt.)
X PixMap compatible matrix file
-nmr6 [<.xpm>] (nmr6.xpm) (Opt.)
X PixMap compatible matrix file
-noe [<.dat>] (noe.dat) (Opt.)
Generic data 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)
-[no]w (no)
View output .xvg, .xpm, .eps and .pdb files
-xvg <enum> (xmgrace)
xvg plot formatting: xmgrace, xmgr, none
-nlevels <int> (40)
Discretize RMS in this number of levels
-max <real> (-1)
Maximum level in matrices
-[no]sumh (yes)
Average distance over equivalent hydrogens
-[no]pbc (yes)
Use periodic boundary conditions when computing distances
主父萱17094328159： 還有mVpp mVrms errore in tensione errore di fase@60°是什么意思 -
錯(cuò)那縣機(jī)械： ______[答案] 1、mVpp是信號(hào)電壓幅度的單位,要是真的用用漢語(yǔ)就是峰峰值的電壓是多少毫伏的. 2、mVrms是連續(xù)承受最大電壓是多少毫伏 3、errore?error吧,error in tensioner:張力裝置中的錯(cuò)誤 di?是data input嗎,就是數(shù)據(jù)輸入 fase沒(méi)這個(gè)詞吧 很費(fèi)勁,...
主父萱17094328159： 功放 PROT閃爍是什么意思 -
錯(cuò)那縣機(jī)械： ______[答案] 功率放大器的主要技術(shù)指標(biāo) 1.輸出功率 ( l)額定輸出功率:即RMS功率.在放大器頻率特性與諧波失真系數(shù)均能達(dá)到規(guī)定的技術(shù)指標(biāo)下(普通功放失真度小于1%,高保真功放失真度小于0.1%),功率放大器所能輸出的連續(xù)正弦波信號(hào)功率. (2...
主父萱17094328159： 誰(shuí)能解讀一下功放說(shuō)明書(shū)上的這些意思~12V電壓4歐時(shí)額定功率 2 x 120 Watts RMS13,8 V 電壓4歐額定功率/最大功率 2 x 150/250 Watts RMS/Music13.8V電... -
錯(cuò)那縣機(jī)械： ______[答案] 這些標(biāo)準(zhǔn)實(shí)際只告訴你: 在輸出峰值多少伏時(shí) 在多大音箱電阻的情況下 它們的音樂(lè)功率是多少! 其中的某某某伏是輸出電壓! 某某歐是負(fù)載的電阻! --寂寞大山人
主父萱17094328159： 眶內(nèi)橫紋肌肉瘤(RMS)的組織學(xué)分類是什么樣的?
錯(cuò)那縣機(jī)械： ______ 眶內(nèi)橫紋肌肉瘤(RMS)在組織學(xué)上分為三組:胚胎型,腺泡型, 及多形型.胚胎型又分為經(jīng)典型,葡萄狀型,棱形細(xì)胞型及間變型. 胚胎型以兒童最多見(jiàn).多形性的多發(fā)生在年齡較長(zhǎng)的成人.葡萄狀 屬RMS接近粘膜表面(如結(jié)膜).腺泡型多累友眶底,預(yù)后最差. 最近根據(jù)研究小組(IRS)顯示更積極的治療可使預(yù)后接近胚胎型.
主父萱17094328159： 真有效值采集器的真有效值從實(shí)用角度定義是什么?
錯(cuò)那縣機(jī)械： ______ RMS即真有效值,是對(duì)交流信號(hào)幅度的基本量度,可以分別從實(shí)用角度和數(shù)學(xué)角度予以定義. 從實(shí)用角度定義是:一個(gè)交流信號(hào)的真有效值等于在同一電阻性負(fù)載上產(chǎn)生同等熱量所需的直流量.例如,1V真有效值交流信號(hào)與1V直流信號(hào)在同一電阻上產(chǎn)生的熱量相同.
主父萱17094328159： J2ME中RMS的使用解析是什么?
錯(cuò)那縣機(jī)械： ______ 轟的一聲巨響,天上掉下神仙水一滴,化作一個(gè)冰封神劍,恭喜!恭喜啊! 在J2ME中,RMS作為唯一的永久性存儲(chǔ)工具,其重要性是不言而喻的.但是很多剛剛開(kāi)始學(xué)習(xí)...
主父萱17094328159： 汽車音響存在什么問(wèn)題呢?
錯(cuò)那縣機(jī)械： ______ 3.輸出功率,功率問(wèn)題最令汽車音響從業(yè)人員認(rèn)識(shí)不清,在這里需要一一講解:A、額定輸出功率,稱為(RMS),指放大器輸出的音頻信號(hào)在總諧波失真范圍內(nèi),所能輸出的最大功率
主父萱17094328159： mVpp表示什么意思物理上謝謝很急啊還有mVppmVrms謝謝
錯(cuò)那縣機(jī)械： ______ 1、mVpp是信號(hào)電壓幅度的單位,要是真的用用漢語(yǔ)就是峰峰值的電壓是多少毫伏的. 2、mVrms是連續(xù)承受最大電壓是多少毫伏 3、errore?error吧,error in tensioner:張力裝置中的錯(cuò)誤 di?是data input嗎,就是數(shù)據(jù)輸入 fase沒(méi)這個(gè)詞吧 很費(fèi)勁,大哥,看清楚了再發(fā)啊
主父萱17094328159： 域外飛鷹刮光技術(shù)是怎么回事???作為另一種組合,可以將壓制刀片
錯(cuò)那縣機(jī)械： ______ PCBN刮光刀片,這是一種裝在刀尖后面的一條平的刀刃,用來(lái)提高零件表面質(zhì)量.... 很多工序采用磨削,規(guī)定表面粗糙度要達(dá)到16rms或更好(rms表示為均方根值). ...
gmx rms -f *.xtc -s *.tpr -o *_rmsd.xvg -m *_rmsd.xpm -tu ns
gmx rmsf -f *.xtc -s *.tpr -oq *_bfactor.pdb(默認(rèn)寫(xiě)到-s文件中，或者用-q提供一個(gè)新的pdb寫(xiě)入bfactor) -o *_rmsf.xvg -res(一定要加，否則算的是atom的)
幾個(gè)概念：rmsd vs rmsf vs rmsdist
RMSD 是對(duì)原子總數(shù)求平均， RMSF 是對(duì)單個(gè)原子時(shí)間求平均
RMSD表示的是分子結(jié)構(gòu)變化的程度，而RMSF值表示的是分子中各個(gè)原子運(yùn)動(dòng)的自由程度
rmsd
計(jì)算的是某個(gè)結(jié)構(gòu)（N個(gè)原子）相對(duì)于參考結(jié)構(gòu)（-s指定）的 root mean square deviation
rmsf
計(jì)算的是一個(gè)原子在一段時(shí)間的平均，和bfactor有關(guān)
rmsdist 計(jì)算的是原子i和j直接的距離隨時(shí)間的變化大小，rmsd算的是原子i相對(duì)自己的位置變化大小
OPTIONS
Options to specify input files:
-s [<.tpr/.gro/...>] (topol.tpr) //參考結(jié)構(gòu)reference structure
Structure+mass(db): tpr gro g96 pdb brk ent
The reference structure is taken from the structure file (-s).
-f [<.xtc/.trr/...>] (traj.xtc)
Trajectory: xtc trr cpt gro g96 pdb tng
Each structure from a trajectory (-f) is compared to a reference structure.
-f2 [<.xtc/.trr/...>] (traj.xtc) (Opt.) //算矩陣的時(shí)候，默認(rèn)是第一個(gè)trj和第一個(gè)trj每一幀計(jì)算rmsd，用-f2則是第一個(gè)trj和第二個(gè)trj每一幀比較rmsd
Trajectory: xtc trr cpt gro g96 pdb tng
With -f2, the 'other structures' are taken from a second trajectory, this generates a comparison matrix of one trajectory versus the other.
-n [<.ndx>] (index.ndx) (Opt.)
Index file
Options to specify output files:
-o [<.xvg>] (rmsd.xvg)
xvgr/xmgr file
-mir [<.xvg>] (rmsdmir.xvg) (Opt.) // the mirror image of the reference structure 不需要
xvgr/xmgr file
With option -mir also a comparison with the mirror image of the reference structure is calculated. This is useful as a reference for 'significant' values, see Maiorov & Crippen, Proteins 22, 273 (1995).
-a [<.xvg>] (avgrp.xvg) (Opt.) 不需要
xvgr/xmgr file
-dist [<.xvg>] (rmsd-dist.xvg) (Opt.) 不需要
xvgr/xmgr file
-m [<.xpm>] (rmsd.xpm) (Opt.)
X PixMap compatible matrix file
Option -m produces a matrix in .xpm format of comparison values of each structure in the trajectory with respect to each other structure . This file can be visualized with for instance xv and can be converted to postscript with gmx xpm2ps.
-bin [<.dat>] (rmsd.dat) (Opt.)
Generic data file
Option -bin does a binary dump of the comparison matrix .
-bm [<.xpm>] (bond.xpm) (Opt.) //角度的矩陣
X PixMap compatible matrix file
Option -bm produces a matrix of average bond angle deviations analogously to the -m option. Only bonds between atoms in the comparison group are considered.
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
gmx rms compares two structures by computing the root mean square deviation (RMSD), the size-independent rho similarity parameter (rho) or the scaled rho (rhosc), see Maiorov & Crippen, Proteins 22, 273 (1995). This is selected by -what
-[no]pbc (yes)
PBC check
-fit <enum> (rot+trans) //默認(rèn)rot+trans，不需要
Fit to reference structure: rot+trans, translation, none
Option -fit controls the least-squares fitting of the structures on top of each other: complete fit (rotation and translation), translation only, or no fitting at all.
-prev <int> (0) //而不是ref
Compare with previous frame
Option -prev produces the comparison with a previous frame the specified number of frames ago.
-[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) 不需要
Use mass weighting for superposition
Option -mw controls whether mass weighting is done or not. If you select the option (default) and supply a valid .tpr file masses will be taken from there, otherwise the masses will be deduced from the atommass.dat file in GMXLIB. This is fine for proteins, but not necessarily for other molecules. A default mass of 12.011 amu (carbon) is assigned to unknown atoms. You can check whether this happened by turning on the -debug flag and inspecting the log file.
-nlevels <int> (80) //xpm為的z分80個(gè)level,不需要改
Number of levels in the matrices
-ng <int> (1) //意思可能是可以算兩個(gè)grp的rms
Number of groups to compute RMS between
OPTIONS
Options to specify input files:
-f [<.xtc/.trr/...>] (traj.xtc)
Trajectory: xtc trr cpt gro g96 pdb tng
-s [<.tpr/.gro/...>] (topol.tpr) // a reference frame
Structure+mass(db): tpr gro g96 pdb brk ent
gmx rmsf computes the root mean square fluctuation (RMSF, i.e. standard deviation) of atomic positions in the trajectory (supplied with -f) after (optionally) fitting to a reference frame (supplied with -s).
-n [<.ndx>] (index.ndx) (Opt.)
Index file
-q [<.pdb>] (eiwit.pdb) (Opt.)
Protein data bank file
Options to specify output files:
-oq [<.pdb>] (bfac.pdb) (Opt.) //計(jì)算并保存B-factor values到-s提供的結(jié)構(gòu)中 或者 可以用-q提供一個(gè)新的pdb結(jié)構(gòu)
Protein data bank file
With option -oq the RMSF values are converted to B-factor values, which are written to a .pdb file. By default, the coordinates in this output file are taken from the structure file provided with -s,although you can also use coordinates read from a different .pdb file provided with -q. There is very little error checking, so in this caseit is your responsibility to make sure all atoms in the structure file and .pdb file correspond exactly to each other.
-ox [<.pdb>] (xaver.pdb) (Opt.) //計(jì)算并保存B-factor values到平均結(jié)構(gòu)中
Protein data bank file
Option -ox writes the B-factors to a file with the average coordinates in the trajectory.
-o [<.xvg>] (rmsf.xvg)
xvgr/xmgr file
-od [<.xvg>] (rmsdev.xvg) (Opt.) //和rmsf算出來(lái)的一樣，沒(méi)用
xvgr/xmgr file
With the option -od the root mean square deviation with respect to the reference structure is calculated.
-oc [<.xvg>] (correl.xvg) (Opt.)
xvgr/xmgr file
-dir [<.log>] (rmsf.log) (Opt.)
Log file
With option -dir the average MSF (3x3) matrix is diagonalized. This shows the directions in which the atoms fluctuate the most and the least.
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)
-[no]w (no)
View output .xvg, .xpm, .eps and .pdb files
-xvg <enum> (xmgrace)
xvg plot formatting: xmgrace, xmgr, none
-[no]res (no) //一定要
Calculate averages for each residue
-[no]aniso (no) //各向異性溫度因子
Compute anisotropic termperature factors
With the option -aniso, gmx rmsf will compute anisotropic temperature factors and then it will also output average coordinates and a .pdb file with ANISOU records (corresonding to the -oq or -ox option). Please note that the U values are orientation-dependent, so before comparison with experimental data you should verify that you fit to the experimental coordinates. When a .pdb input file is passed to the program and the -aniso flag is set a correlation plot of the Uij will be created, if any anisotropic temperature factors are present in the .pdb file.
使用-aniso選項(xiàng)，gmx rmsf將計(jì)算各向異性溫度因子，然后它還將輸出平均坐標(biāo)和帶有ANISOU記錄的.pdb文件(與-oq或-ox選項(xiàng)相對(duì)應(yīng))。請(qǐng)注意U值是與方向相關(guān)的，因此在與實(shí)驗(yàn)數(shù)據(jù)進(jìn)行比較之前，您應(yīng)該驗(yàn)證您是否適合實(shí)驗(yàn)坐標(biāo)。當(dāng)將.pdb輸入文件傳遞給程序并設(shè)置-aniso標(biāo)志時(shí)，如果.pdb文件中存在任何各向異性溫度因子，則會(huì)創(chuàng)建Uij的相關(guān)圖。
-[no]fit (yes)
Do a least squares superposition before computing RMSF. Without this you must make sure that the reference structure and the trajectory match.
computes the root mean square deviation of atom distances , which has the advantage that no fit is needed like in standard RMS deviation as computed by gmx rms. The reference structure is taken from the structure file.
The RMSD at time t is calculated as the RMS of the differences in distance between atom-pairs in the reference structure and the structure at time t.
gmx rmsdist can also produce matrices of the rms distances , rms distances scaled with the mean distance and the mean distances and matrices with NMR averaged distances (1/r^3 and 1/r^6 averaging). Finally, lists of atom pairs with 1/r^3 and 1/r^6 averaged distance below the maximum distance (-max, which will default to 0.6 in this case) can be generated, by default averaging over equivalent hydrogens (all triplets of hydrogens named *[123]).
OPTIONS
Options to specify input files:
-f [<.xtc/.trr/...>] (traj.xtc)
Trajectory: xtc trr cpt gro g96 pdb tng
-s [<.tpr/.gro/...>] (topol.tpr)
Structure+mass(db): tpr gro g96 pdb brk ent
-n [<.ndx>] (index.ndx) (Opt.)
Index file
-equiv [<.dat>] (equiv.dat) (Opt.)
Generic data file
Additionally a list of equivalent atoms can be supplied ( -equiv), each line containing a set of equivalent atoms specified as residue number and name and atom name;
e.g.: HB* 3 SER HB1 3 SER HB2. //可能第一列要給距離命名
Residue and atom names must exactly match those in the structure file, including case. Specifying non-sequential atoms is undefined.
此外，還可以提供等效原子列表(-equiv)，每行包含一組等效原子，這些原子指定為殘基編號(hào)和名稱以及原子名稱;例如:HB* 3 SER HB1 3 SER HB2。殘基編號(hào)和原子名稱必須與結(jié)構(gòu)文件中的名稱完全匹配，包括case。未定義指定非順序原子。
Options to specify output files:
-o [<.xvg>] (distrmsd.xvg)
xvgr/xmgr file
-rms [<.xpm>] (rmsdist.xpm) (Opt.)
X PixMap compatible matrix file
-scl [<.xpm>] (rmsscale.xpm) (Opt.)
X PixMap compatible matrix file
-mean [<.xpm>] (rmsmean.xpm) (Opt.)
X PixMap compatible matrix file
-nmr3 [<.xpm>] (nmr3.xpm) (Opt.)
X PixMap compatible matrix file
-nmr6 [<.xpm>] (nmr6.xpm) (Opt.)
X PixMap compatible matrix file
-noe [<.dat>] (noe.dat) (Opt.)
Generic data 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)
-[no]w (no)
View output .xvg, .xpm, .eps and .pdb files
-xvg <enum> (xmgrace)
xvg plot formatting: xmgrace, xmgr, none
-nlevels <int> (40)
Discretize RMS in this number of levels
-max <real> (-1)
Maximum level in matrices
-[no]sumh (yes)
Average distance over equivalent hydrogens
-[no]pbc (yes)
Use periodic boundary conditions when computing distances
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