improper
dihedral

By convention, the first atom of an improper
dihedral (type A-X-X-B or A-B-C-D) is usually the central atom.  This had
been a general rule in the past.

2014-06-19

原文摘錄自：CHARMM c32b2 parmfile.doc

[筆記]VMD/NAMD命令/規(guī)則

(2013-10-10 16:18:42)

標(biāo)簽： vmd namd 筆記

分類： 分子模擬

添加周期性水環(huán)境
package require solvate
solvate ubq.psf ubq.pdb -t 5 -o ubq wb
-t (override with any of the following)
-o (data will be written to output.psf/output.pdb)
添加離子中和多余電荷
autoionize -psf file.psf -pdb file.pdb  [options]
可以直接使用VMD中extension>modeling>add ions的autoionize完成
TK console中選擇全部原子，保存psf與pdb文件
參考：Autoionize Plugin
命令模式運行ubq.pgn
> vmd -dispdev text -e ubq.pgn
測量周期最大最小邊界
set everyone [atomselect top all]
measure minmax $everyone
測量周期中心點
set everyone [atomselect top all]
measure center $everyone
測量質(zhì)量中心
measure center $sel weight mass
位置移動
atomselect0 moveby {1 1 6}   # 把所選原子向1，1，6向量方向和距離上移動
atomselect0 moveto { 3 6 5}  # 把所選內(nèi)容移動到3，6，5位置
原文：VMD的TK Console中的內(nèi)置命令
設(shè)置resname/chain/resid
mol load pdb fileA.pdb
set sel [atomselect top "serial <=9"]
$sel set resname CD
$sel set chain X
$sel set resid 8
set all [atomselect top all]
$all writepdb fileB.pdb
refer the VMD Graphical Representations>Selections>Keyword for more values
top文件
IC A B C D [bond(AB)] [angle(ABC)] [dihedral(ABCD)] [angle(BCD)] [bond(CD)]
IC A B *C D [bond(AC)] [angle(BCA)] [improper(ABCD)] [angle(BCD)] [bond(CD)].
The * next to the C atom indicates that it is at the center of an improper angle definition. No * indicates that the 4 atoms do not have an improper topology.
Specifying IC’s is not necessary if you already have all the atoms in your PDB file. The entries are simply there
to have a way to create missing atoms from the positions of present ones.
參考：NAMD topology-tutorial
VMD鍵長單位
number in the “Value” field corresponds to the length of the bond in ?ngstroms.
reference:Using VMD - An Introductory Tutorial
psfgen命令
pdbalias residue HOH TIP3 #aliasing residue HOH to TIP3
pdbalias atom TIP3 O OH2 #aliasing residue TIP3 atom O to OH2
vmd中tk命令打開文件
mol new filename.psf       #打開一個文件
mol addfile filename.pdb #打開另一個文件，并疊加到第一個文件結(jié)構(gòu)上
最適分子數(shù)
Presently, the maximum number of atoms one can expect to realistically compute with high level quantum chemistry is approximately 120 atoms
平衡態(tài)模擬
常見的模擬思路是，先在NVT下約束住你的溶質(zhì)（劑）做限制性模擬，這是一個升溫的過程，當(dāng)溫度達(dá)到你的設(shè)定后, 接著做NPT模擬，此過程將調(diào)整體系的壓強進(jìn)而使體系密度收斂。
經(jīng)過一段時間的平衡模擬，在確定系統(tǒng)弛豫已經(jīng)完全消除之后，就可以開始取數(shù)據(jù)了。如何判斷體系達(dá)到平衡，簡單的講可以通過以 下幾種方式，一，看能量（勢能，動能和總能）是否收斂；二，看系統(tǒng)的壓強，密度等等是否收斂；三看系統(tǒng)的RMSD是否達(dá)到你能接受的范圍，等等。
升溫/降溫控制
# IF Heating
reassignFreq 2000
reassignTemp 100
reassignIncr 1
reassignHold 300
#從100K升溫到300K，每2000步升高1K

# IF Cooling
reassignFreq 2000
reassignTemp 300
reassignIncr -1
reassignHold 100
 固定分子
all atoms with a value of 1 (or a number different of 0) in a predetermined column will be fixed; atoms with a value of 0 in the same column will not be affected.
load pdb file into the psf file in vmd
in TKcon
set allatoms [atomselect top all]
$allatoms set beta 0
set fixedatom [atomselect top "resid 1 and name CA"]
$fixedatom set beta 1
$allatoms writepdb fileName.ref
拉動原子
to set which atom is to be pulled (SMD atom).uses the occupancy column of the pdb file to distinguish it
set allatoms [atomselect top all]
$allatoms set occupancy 0
set smdatom [atomselect top "resid 76 and name CA"]
$smdatom set occupancy 1
$allatoms writepdb fileName.ref
牽拉方向
set smdpos [lindex [$smdatom get {x y z}] 0]
set fixedpos [lindex [$fixedatom get {x y z}] 0]
vecnorm [vecsub $smdpos $fixedpos]
run a NAMD simulation
namd2 +p[procs] configfile > outfile
力場中二面角倒序正序區(qū)別
軟件里的二面角有正負(fù)是得考慮4號原子在123號原子平面的哪一側(cè)，舉MS里二面角的來說，按順序點1234共4個原子，二面角指的是123平面和234 平面的二面角，沿著23的軸看過去，1號原子在4號原子的逆時針方向（左手邊），則取正值，反之取負(fù)值；絕對值仍在[0,180]。
原文摘錄自：二面角和扭轉(zhuǎn)角區(qū)別
Reversing the atoms in a proper dihedral does not have any mathematical or practical consequences. Conversely, the ordering of the atoms is very important for improper dihedrals.
原文摘錄自：Parameters for a Protein-RNA covalent bond

力場參數(shù)圖示
2014-06-18
圖片來源：Brève introduction à la mécanique (MM) et à la dynamique moléculaire (DM)

improper
dihedral

By convention, the first atom of an improper
dihedral (type A-X-X-B or A-B-C-D) is usually the central atom.  This had
been a general rule in the past.

2014-06-19

原文摘錄自：CHARMM c32b2 parmfile.doc

拓?fù)湮募嗀UTOGENERATE ANGLES DIHEDRAL
AUTOgenerate default options to be used when building a sturcture.AUTO ANGLes specifies that all possible angles and DIHEdral specifies that all possible dihedral angles be generated when building a structure.  If these options are not included the angles and/or dihedrals must be listed explicitly in the topology file
2014-06-19
原文轉(zhuǎn)自：CHARMM c38b1 rtop.doc

namd開始NPT計算過程報錯Periodic cell has become too small for original patch grid解決方法

I have a different approach to fixing this problem. I believe that the underlying cause of this error is that the system is resizing too quickly (due to the system pressure being far from the specified pressure). To slow the resizing down I increase langevinPistonPeriod to 1000 and langevinPistonDecay to 500 for a short time when I start the NPT simulation, and then switch to the normal values of 100 and 50.

For example, in your case I would do one input file for 100 ps with a constraintscaling of 10, langevinPistonPeriod of 1000, and a langevinPistonDecay of 500. Then I would load the restart files into a new simulation and proceed as you were above. Also, by restarting the simulation you are forcing NAMD to re-assign the patches, which will help prevent this error.
2014-08-26
原文摘錄自：Re: Periodic cell has become too small for original patch grid!
FATAL ERROR: Periodic cell has become too small for original patch grid!
問題出現(xiàn)在nvt計算完成后第一次進(jìn)行npt的時候.通過在namd的郵件列表尋找，最后發(fā)現(xiàn)是周期性盒子設(shè)置的時候四舍五入數(shù)值，造成盒子在npt計算 過程中溶劑環(huán)境密度過?。ê凶芋w積過大，而分子總數(shù)一定，最終水溶液密度過低）。解決方法，周期盒子大小不能直接四舍五入，要考慮到盒子體積與分子總數(shù)得 到溶液的密度是否恰當(dāng)好處。改用該方法后，順利計算，為提示錯誤。
2014-9-10
該內(nèi)容原創(chuàng)

計算namd體系密度
首先計算體系的質(zhì)量，然后根據(jù)namd輸出的體積，兩者相除即可。過程如下：
例如：
C     11
H     1596
O     790
N     2
上面表示的是每種原子的個數(shù)
則mass=（11*12+1596*1+790*16+2*14）/NA 單位為克。
NA為阿伏伽德羅常數(shù)：6.02214129(27)×10²³
那么密度為mass/V
2014-08-26
原文摘錄自：heating過程中水盒子形狀發(fā)生變化


VMD計算SASA(solvent-accessible surface area )
控制臺下用命令即可得出：
set all [atomselect top "all"]
set some [atomselect top "resid 1 to 5"]
measure sasa 1.4 $all -restrict $some -points sasapoints
foreach pt $sasapoints {
  draw point $pt
}
以上可以在窗口中顯示出1-5號氨基酸的溶劑可及表面，以point繪出。當(dāng)然如果不需要瀏覽僅僅計算的話，只需要：
set all [atomselect top "all"]
set some [atomselect top "resid 1 to 5"]
measure sasa 1.4 $all -restrict $some
如果想看一下準(zhǔn)不準(zhǔn)可以算一下除了1-5號氨基酸的是多少
set someothers [atomselect top "not(resid 1 to 5)"]
measure sasa 1.4 $all -restrict $someothers
將兩個值相加，看是否是
measure sasa 1.4 $all
得到的結(jié)果。
2014-9-10
原文摘錄自：關(guān)于溶劑可及表面積（Solvent Accessible Surface）- Biocheming
try VMD timeline Tool to calculate the change in SASA over time.
Load the molecule and trajectory and then go to:
Extensions -> Analysis -> Timeline.
SASA is one of the many parameters you can calculate in the Timeline window.
2014-9-10
原文摘錄自：How to calculate solvent accessible surface (SASA)?-Uttam Pal