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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 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(yùn)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(diǎn) 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} atomselect0 moveto { 3 6 5} 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 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(qiáng)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(qiáng)，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 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(diǎn)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 ![[筆記]VMD/NAMD命令/規(guī)則](http://image109.360doc.com/DownloadImg/2015/01/3109/49685599_2_20230519040722303.jpeg "[筆記]VMD/NAMD命令/規(guī)則") 2014-06-18圖片來源：Brève introduction à la mécanique (MM) et à la dynamique moléculaire (DM) improper dihedral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. 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. 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 H O N 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 { } 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
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 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(yùn)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(diǎn) 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} atomselect0 moveto { 3 6 5} 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 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(qiáng)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(qiáng)，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 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(diǎn)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. 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. 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 H O N 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 { } 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 |
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(2013-10-10 16:18:42)
