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MACROBUTTON MTEditEquationSection2 Equation Chapter 1 Section 1 SEQ MTEqn \r \h \* MERGEFORMAT SEQ MTSec \r 1 \h \* MERGEFORMAT SEQ MTChap \r 1 \h \* MERGEFORMAT GROMACS TutorialComputational Photodynamics Research LaboratoryLast edited: 2nd Nov 2017GROMACS(GROningen MAchine for Chemical Simulations) ? ????? Groningen University?? ?? ???? ?? ???? ?? ?? ???(Molecular Dynamics: MD) ???? ‘???’??. GROMACS? ??? ????? ???? ?? ?????? ??? ???? ?? ??? ??? ?? ? ??, ??? ??? ??, ?? ??? ???? ???.1. GROMACS ??? ???? gromacs-5.1.5 ??? ???? ?????. Gromacs ?????? groamcs-5.1.5.tar.gz? ?? ? ??? ????. ?? ?? ?? INSTALL? ?? ?? ?? ???? ??? ?? ? ? ??.? ? cmake? ???? ???? ?? ????? ?????? ??? ????, install directory? ??? ?? option? ?? ??, ??? ???? ?? ?? ?? ???? ?? ?? ????. ? ??? Linux? ?? ??? ?? ?? ?????, ??? ???? ????? ??. ????? ? ?? option? ??? ????? ??.-DCMAKE_C_COMPILER ????? ??? ??? ??.-DGMX_DOUBLE=ON ????? ???? double precision? ????.-DMKL_INCLUDE_DIR=???? mkl library? ??? ?????.-DCMAKE_INSTALL_PREFIX= ??? binary ??? ??? ?????.-DGMX_THREAD_MPI=OFF thread_mpi ??? ???? ???. Parallel ??? ???? ??? ?? ????? mpicc? ?? ? ??? ??? ?????.-DGMX_MPI=ON Configuration? ????? ?????? INSTALL? ?? ?? makemake checkmake install? ???? ??? ? ??? gromacs binary? ??? ??? ????? ??.2. GROMACS ?? ??2-1. GROMACS? ??? ?? ??? ?????? ??GROMACS? ??? directory ??? /bin?? ??? ??? ?????? ??? ??. ??? binary?? ??? ??? ??????. ???? ?? ??? ?? -h ??? ?? ???? (?: gmx grompp -h, gmx mdrun -h) ??? ?????? ?? ??? ???? ?? ???? ??? ? ??. ????? GROMACS manual? ??? ?? ?? ????, ??? ???? ???? ???? ????? ???? ?? ? ?? ?? ?? ??? ? ???. ?? ~/.cshrc ? PATH ??? GROMACS ?????? ??? directory? ??? ???? ??? ???? ??? (???? ????).MD ?????? ???? ??? ???? ???? ???? ??? ????. ?? ??? ???? ??????? ?? ??? ??? ? ??? ???? ?????? ?? 1? ????? ??. ???? ????? ??? ??? ?? ?? ?????? ???? ?? ? ? ??. ??? ?? ????? ??? 5??? ?????? ??? ? ?? ????? ??.?? 1. ???? ?? ??? ??????? ?? flow chart(??: GROMACS ????)?? MD ?????? ??? ?? ??? ?????.- System? ??- Energy minimization- Solvation- Energy minimization of solvated system- Heating and equilibration- Production and data analysis?? NVT ?????(Canonical ensemble)? ? ?? system? ?? ??? ?? ? ? thermostat? ?? temperature coupling? ??. ? ? ?? ?? ?????? ?? equilibration? ? ? ?? production? ?? ? ?????? ??? ??. Heating? production? ???? ?? MD? ???? ???? ??? ??? ???(trajectory)? ???? ?? ?? ???? ??? equilibration? ??? ?? ??.2-2. GROMACS?? ???? ???? ?? ??GROMACS?? ???? ????? ??? ?? ??? (???) ???? ?? ?? ??? GROMACS? ?? ??? ??????? ????? ?? ??. ? ???? ?? ???? ???? ??? ????? ????. ??? ??? ???? force field? ??? ??? ?? ?????? ??? ???, ???? ???? ????.- pdb ??pdb ???? ???? ?? ?? ???? ?? ??. ? ? ?? ??? ?? ???? ???? ?? ???? ??? amino acid residue? ?? ?? ???. ?? ?? MD ????? program?? ?? ???? ??? ????, ?? ?? ?????? ??? ?? ?? ?? pdb ??? GROMACS? ???? ?? ??? format?? ??? ?? ? ???. RCSB protein data bank () ?? ??? ????? pdb ??? ???? ???? ? ??.- gro ??GROMACS? pdb2gmx?? ????? ?? pdb ??? gro ??? top ????? ? ?? ??? ???? ????. ? ? gro ???? system? ???? ???? ??? ?? ???, ? ??? nanometer??. gro ??? pdb ??? ????? ?? ? ?? ?? ???, ?????? ???? ??? ?? ??? ?? ??.- top ??top ???? ??? ???? ?? ??? ??? ?? ??? connectivity, ? ?? ????? bond, angle, dihedral? ???? ???? ?? ??? ?? ??. GROMACS? ?? ???? force field? system? ????? ?????? ? ? ??? ??? ??. ?? ???? ??? ??(ex. water), itp ??? ??? ??? ? #include ??? ?? top file? ????? ??. GROMACS?? ???? ???? itp file?? <GROMACS_dir>/share/gromacs/top? ???? ??.- tpr ??tpr ??? gro ??? top ??? ?? ??? ??? interaction parameter (??/?? ???, ??, Lennard-Jones coefficient ?) ? ?????? ??? ?? option? (?? mdp ??? ??)? ??? ??? ??? ???? ???. tpr ??? ??? (binary) ??, ? ??? ??? ??? ??? input ?? MD ?????? ??? ? ??.- mdp ???????? ?? ?? ?? ???? ?? ?? ????. ???? ??? ?????? ??, ?????? ??, ???? ?? ??, time step ???. ???? ???? ?? ?? ????? ??.- cpt ??cpt? checkpoint? ????, ?????? ??? ?????? ?? ???? ?? ???? ?? ? ???? ????.- edr, trr ??MD ?????? ???? ???? binary??. edr ???? system? ???? ??? ??, ??? trr ???? system? trajectory, ? ??? ??? ???? ???? ?? ???? ??? ??? ?? ??? ?? ??. ?????? ???? ?? ?? ???? system? ??? ?? ??? ?????, ??? ?? ????? ?? ??? ?? ???? mdp ???? ????. ??? ?? ??? ??? ?? ?????? ? ? ??.2-3. GROMACS top ??? ??GROMACS ???? ???? ?? ??? ? top ??? system? interaction function? ?? ??? ?? ?? ?? ??? ? ??? ???? ?? ?? ????. ??? ??? system? ???? ??? ?? interaction function? GROMACS library?? ?? ?? force field file? ???? ???, ??? ?? ???? ??? interaction function? ?????? ?? ? ??? top file? ?? ?????? ? ?? ??. ??? top file? ??? ???? ?? ?????. ??? ??? gmxexercise.tar? urea??? ??? ? ??? ??? ??? ??. ??? ???? .mdp, .gro, .top??? ???? .tpr??? ????? ??? ??? ?? -pp??? ????? ??? ?? ? ??. ??? ???? .top??? ???? .itp??? ??? ??? ????.gmx grompp –f urea.mdp –c urea.gro –p –o urea.tpr –pp ?? ? ?? top file? ? section? ??? ????? ????. ??? ??? GROMACS MANUAL(section 5, Table 5.4-5.5)? ????.[ defaults ] ?? ?? nonbonded interaction? ?? ??? ?? ?? ????. nbfunc? nonbonded interaction? ??? ???? ??? 1? Lennard-Jones??. comb-rule? combination rule? ??? atomtype?? ?????. gen-pairs? pairs interaction? ??? ??? Lennard-Jones parameter? ??? ???? ?? ???? yes? ?? LJ interaction? ????. fudgeLJ? fudgeQQ? Lennard-Jones interaction? electrostatic interaction? scale factor??.[ atomtypes ] Atom? ??? mass, number, ??? Lennard-Jones parameter? ????. ?? atom??? connect? ?? atom? ?? ??? ?? ??? ? ???? ????? ???? ??. Lennard-Jones interaction??? ?? ??????? atom? ?? ??? parameter? ??? ? ???, ??? defaults? ??? combination rule? ??? ? atom? parameter? ???? ????.[ bondtypes ] 2 body bond stretching? ?? interaction function? list??. 2?? interaction function? ???? atom name? function type ? function? ??? parameter? ????. ?? ?? ??? function type? Harmonic potential(function type: 1)?? ? ?? Morse, Cubic potential ?? ????.[ pairtypes ] 1-4 bonded LJ interaction? Coulomb interaction? ????. ? interaction? ?? force field?? nonbonded interaction? ??? ???? LJ ? Coulomb interaction???, nonbonded interaction? ??? ??? interaction function? ??, force field ??? ??? scale factor? ?? interaction energy ? force? scale down??.[ angletypes ] 3 body angle bending? ?? interaction function? list??. Bonds? ????? atom name, function type, parameter? ????. ?? ?? ??? function type? ?? Harmonic potential(function type: 1)?? ? ??? Urey-Bradley potential ?? ???.[ constrainttypes ] ?? bond? angle? ??? ???? ? ???? ??? bond? ??? atom name? function type, ??? parameter? ????.[ dihedraltypes ] 4 body dihedral angle? ?? interaction function? list??. Dihedral angle? ?? ???? ? ? ??? proper dihedral(function type: 9)? improper dihedral(function type: 4) ? ??? ???, ?? ?? ?? ????. Bonds, angles? ????? atom name, function type, parameter? ????.?? 2. Dihedral angle? ??. ??? proper, ???? improper dihedral??.(??: PumMa ????)[ implicit_genborn_params ] Implicit solvent? ?? parameter??. Atomname ??? 5?? parameter? ?? ??? ? 3?? ???? ?? 4?? parameter? atom? vdw radii, 5?? parameter? HCT scale factor??. ? ?? ??? dielectric constant ?? top ??? ??? mdp ??? ????.[ moleculetype ] Molecule? definition? ????, molecule? ??? nrexcl??? ??? ????. nrexcl? bond distance ???, nrexcl?? bond?? ?? ?? atom?? nonbonded interaction?? ????. MD? ? step?? ? atom? ?? nonbonded interaction? ? ??? ???? ???, (??? ??? GROMACS MANUAL?? neighbor searching ??) ? ?? nrexcl??? bond distance? ?? atom? ???? ???. ?? ? atom?? ??? ??? interaction function? ?? bonded interaction? ?? ??. ???? ?? nrexcl? ?? 3?? ????. [ atoms ] molecule?? ?? ? atom? ?????. ? atom? ??? residue ??/??, atom ?? ? charge group number, ????? atomic partial charge ??? ????. Atomic partial charge? Coulomb interaction? ????? ???? ??? top file? ?? ???? ???? ?? ????. (??, vdw interaction? force field ?? ??? parameter? ????? ?? ? ??.)[ bonds ] [ pairs ] [ angles ] [ dihedrals ] ?? atom index? function type? ?????, ??? ?? function type? ????? ??. ??? ??? parameter? ?? ??? types??? ????.?? ???? top??? ?? ?? ??? ? ???? ?? ???? ??? ??? ??? ??? parameter??? ???? types???? itp ??? ?? ????, ??? include ?? ???? ????.2-4. GROMACS?? potential energy ?? ???? ???? ?? ???? ?? ???? ???? GROMACS?? ??? potential energy? ?????? ????. GROMACS?? ???? potential energy function? bonded interaction? non-bonded interaction? ??? ??? ? interaction? ?? ?? ???? ????. ???? MD ??????? potential? ??? ??? ???? ???, mdrun ??? input ??? tpr ??? ?? ???? ????. ?? ?? binary ??? tpr ??? ??? ??? ????.gmx dump –s urea.tpr > tpr.txtgmx dump ???? ???? .edr, .trr? ?? binary?? ?? ??? ??? ???? ?? ? ??.tpr.txt??? ????? ??. tpr.txt ??? ffparams??? ?? ?? potential energy ??? ?? function type? parameters?? ?? ??.atnr? atomtype? ??? ??? ntypes? ??? potential energy function? ??? ????.??? functype? function type? ????? ???? 1,4 Lennard-Jones potential fuction? ??? Lennard-Jones potential function(LJ_SR)? ??, bond(BONDS), angle(ANGLES), proper dihedral(PDIHS), improper dihedral(PIDIHS), 1,4 Lennard-Jones potential(LJ14) ??? ?? function type? ??? ??. ?? ? function type??? potential fuction ??? ??? parameters? ?? ??. ? ???? ???? MD ?????? ?? ? potential energy ??? ??? bonded interaction? ??, tpr??? Bond: section?? ??? ? interaction? ?? ???? ???? index? ???? function type? parameters? ?? ??? ffparams: section? ???? ??.Bond: nr: 21 iatoms: 0 type=16 (BONDS) 0 1 1 type=17 (BONDS) 0 2 2 type=17 (BONDS) 0 5?? ?? Non-bonded interaction? bonded interaction? ?? ?? ? ??? interaction?? ?? ???(neighbor)? ? step?? ?? ? ??? ???? ?? ??? tpr ??? ???? ?? MD ??????? ? step ?? on-the-fly? ????. ??? ?? bonded interaction? ?? ?? ????? ??, non-bonded interaction? ?? ??? ? ??? ??. ???, tpr ???? ? ???? ?? ? non-bonded interaction? ??? ?, ???? ???? ?? ???? ????. tpr ??? excls: ??? ?? ??? ???? ?? ???? non-bonded interaction? ???? ?? ?? ???? ??? ?? ?? ??? ? ??. ?? ?? excls[0][0..7]={0,1,2,3,4,5,6,7}? 1? ??? 1,2,3,4,5,6,7,8? ??? non-bonded interaction??? ?? ??? ????.?? non-bonded interaction? ???? ??? ????? ????? ??. 1???? ????? ??? ????? non-bonded interaction? ???? ??? ??. ?? ? ??? ???? cutoff distance?? ???? ?? ???? ?? ??? neighbor list? ????. ? ??? neighbor searching??? ?? neighbor list? ????? ??? ?? cutoff distance? mdp ??? rlist ???? ???? ? ??.???? neighbor list? ???? mdp??? rvdw(distance for columb cutoff)? rcolumb(distance for LJ or Buckingham cutoff)?? ???? ?? ???? van der waals interaction? electrostatic interaction ??? ??. ?? top ??? [defaults] ???? ????? nbfunc? Lennard-Jones potential? ????? van der waals interaction? Lennard-Jones potential? ????, top ??? ?? atomtype??? sigma, epsilon? combination rule? ???? gmx grompp ???? Lennard-Jones parameter(C6, C12)????. ? ?? tpr ??? ffparams ??? function tpye? ?? ??? ??. ??? ???? tpr ??? ???? ???? MD?????? ??? ? step ?? Lennard-Jones potential? ?? ? ? ??. ??? electrostatic interaction? Coulumb potential? ?????? tpr ??? ?? dielectric constant? ? atom? ?? ???? ???? Columb potential ??? ?? ??. ??? ??? Lennard-Jones potential? Coulumb potential? ??? ?? non-bonded interaction? ????. ????? ?? ??? ? step ?? non-bonded interaction? ???? ? ??? ??? ??? ?? ??? ??? ??? neighbor searching?? ?? neighbor ???? ?? ???? ??? cutoff distance ?? ?? ? ??. ??? ??? ?? ?? ?? ?? ?? neighbor seaching? ???? neighbor list? ???? ??? ??? ??? ?? ???? ???? ?? ??? mdp ??? nslist? ????.???? GROMACS?? bonded interaction? non-bonded interaction? ??? ?????? ?????. ?? ??, potential energy? bonded interaction? non-bonded interaction? ???? system? restraint?? external force? ???? ???? ? ???? ???? potential energy? ???? ? ???.4. ?? 1 - Maxwell-Boltzmann ?? ????? ???? ?? ???? ???, ?? ??? ??? 300 K?? NVT-constant ?????? ??? ergodic theorem? ???? ???? ??? ?? Maxwell-Boltzmann ??? ??? ??? ? ???.gmxexercise.tar ??? ??? ?? thermostat, protein, coumarin??? ? ?? ??? ?? ???. ? ? thermostat ??? ????. ?? ??? ? Par.gro? ?? ?? ??? ??? ???? ???? ?????. 3??? ?????, top file?? ??? ??? ??, ??? ?? ??? ?? ??, gro file?? ??? ?? ??? ??? ?? ??. ??? ??? system? ??? ? ?? ?? ???????, ?? ??? kinetic energy? histogram?? ??? ????? ?? distribution? ????? ??? ??.?? mdp ??? ??, ?? ??? ? ?????? ??? ???? ?? ??? ?? ????. ??? parameter?? ???, ??? ??? ??? ?????. ??? simulation input?? ??? ?? ?? ??? ???, ? ?? ????? ?? ??? ?? ???? ????.Integrator – ????? ???? ????. Leap-frog, Velocity-verlet ?? ????? ??.dt – ?????? ???? time step? ??. ??? ps??.steps – ?????? ??? step? ???.nstx(v,f)out – trr ??? x, v, f? ? step?? ???? ????.tcoupl – temperature coupling? ??? thermostat? ??. Berendsen, V-rescale ?? ??? ??.tau-t – temperature coupling? time constant. ?? ??? ?? velocity rescaling? ??? ?? ? ???? ????.ref-t – system? ?? ??? ?? ???? ????.pcoupl – pressure coupling? ??? barostat? ??. Berendsen, Parrinello-Rahman ?? ??? ??.tau-p, ref-p – tau-t, ref-t? ????.epsilon_r – implicit solvent model?? solvent? dielectric constant? ????.coulombtype – electrostatic interaction? ?? ??? ???.vdwtype – Van der Waals interaction? ?? ??? ???.??? 300 K?? 11 ns ?? ?????? ????, ???? ? step?? ??? ???. ???? ?? ??? ??? ??? ?? ??? ?????? ? ?? ????? ????. ???? ??? ????, ??? ???? ????.gmx grompp -f Par.mdp -c Par.gro -p -o Par.tpr -maxwarn 1Center of mass motion? ????? GROMACS ????? ??? ???? ??? ??? ???? ???? ?? ?? ???? ??? ????? ??. -maxwarn 1? ?? 1?? ???? tpr ??? ???? ? ?? ?????.grompp ????? top ??, gro ??, mdp ??? ??? ?????? input ? tpr ??? ?????. ?? ??? ???? ???? mdrun ????? ??? ?? ?????? ????.gmx mdrun -s Par.tpr -e Par.edr -o Par.trr -c Par_out.gro -g Par.logSystem? ??? ?? ?? ???, 11 ns ??? (?????? ????) ??? ? ?????? ?? ?? ??? ?? ??? ??? ?? ?? ? ? ??. ?? 104 ? ??? atom?? ??? system? ??, single core? ??? ?? ??? ? ns ??? ????, multicore ???? ????? ????? load? ?? CPU? ????? ???? ??? ??? ????. ?? ??? ??? non-bonded (coulomb + vdW) interaction ??? ????? ??? ?? ??? ????. ??, bonded interaction? ??? ?? atom ?? ???? ???? ? ??, non-bonded interaction? ??? atom ?? ??? ???? ???? ?? ????.?????? ???? gmx energy ????? ???? edr ????? kinetic energy? ????.gmx energy -f Par.edr -dp -o Par.xvg? ???? ?? component? ?? ?? ????? ???. Kinetic energy? 4????, ?? 4? ???? enter? 2? ???. ??? file? Par.xvg? ?? ?? ? frame?? kinetic energy ??? ??? ?? ? ? ??.?? C ??? ??? ??? ??, ???? ?? 1 ns? ?? 1 ps?? ??? ?? ??? ???? ?? ??? plot? ??. ? ?? system? ???? excess energy? thermostat? ?? ???? equilibration?? ?? ?? ??? ??? ??.??, ???? production ?? (1 ns~11 ns) ? ??? ?? data? ???? histogram? ??? ??. Histogram? ??? 0~30 kJ/mol, ??? ??? 0.02 kJ/mol ? ??, ?? ????? ??? ??? 300 K?? ????? ?? Maxwell-Boltzmann distribution? ????? ????? ????.?? 3. Simulation? ?? ?? Maxwell-Boltzmann distribution? ???? ????, tpr ??? ?? ? ????? ??? ???? center of mass motion? ???? ?? ?? ??????? mdp ??? comm-mode ??? ‘Linear’ ? ??? ?? tpr ??? ??? ?????? ??? ??. ? ???, ???? ???? ???? ????? ??? ??? ?????? ??? ?? ??? ??? ??? ?? ????? ???? ???? ?? ????? ?? ?? ??.????5. ?? 2 - ????? ???? ?? MD ???????? ??? ??? ?? ?????? ? ? ???. ????? ??? ?? ??? ?? ????.????? ??- ??? pdb ????? top ??? gro ??? ???? (vacuum) ???? ?????- Energy minimization- ????? MD ????? (50 ps)- vmd? ??? visualization? analysisPeriodic boundary condition? ??? ??????? ?????- System ??? solvent box ???- ???? ????? energy minimization- ???? ????? MD ????? (50 ps)- vmd? ??? visualization5-1. ????? ??protein ??? ???? ? ?? pdb ??? ?? ???. ?? 2ECH.pdb? RCSB protein data bank?? ??? ???? ?? ????, 2ECH_mod.pdb? ? ? model 6? ????? ??? ?? ?? ???. ?? RCSB?? ?? ???? pdb ??? ??? ?? ?? ????? ??? ????? ???? ??? ?? residue?? ?? ?? ??? ?? ??? ?? ?? ??? ??? ??? ? input?? ??? ? ??. ??gmx pdb2gmx -f 2ECH_mod.pdb? ???? pdb ????? gro ??? top ??? ??? ??. ?? ???? GROMACS? ??? ?? force field?? ??? ?? ?? force field? ??? ??? ?? ???? ???.1: AMBER03 protein, nucleic AMBER94 (Duan et al., J. Comp. Chem. 24, 1999-2012, 2003)2: AMBER94 force field (Cornell et al., JACS 117, 5179-5197, 1995)?? force field?? 8?? CHARMM27 all-atom force field (with CMAP) - version 2.0? ????, water model?? 1?? TIP3P? ????. top? gro ??? ??????, ?? ??? ?? ??? ??? ???? ??? ?? ??? ???? ? conf.gro? ?????. ???? ??? ??? ?? ?? ?? ??? ?? ????.gmx pdb2gmx -f 2ECH_mod.pdb -o 2ECH_mod.gro -p 2ECH_2???? ?????, pdb2gmx -h? ???? ? ???? ?? ??? ????.?? gro ??? top ??? vi editor? ??? ?? ???? ?? ??? ????? ????, ??????? ??? ??? ??? pdb ??? ??? ??. pdb ??? atom? ??? ??? ?? ??? ?? ?? ?? ?? ???, top ??? [ bond ] ? ???? ???? ?? connectivity? ?? ???? force field? ???? ??? ???. gro file? ?? tile line ?? total atom number? ???, ? ?? ? atom? ?? ??? ?? coordinate? ????. top file? ??, ? comment line ?? ??? ?? ??? ?? ??.; Include forcefield parameters#include "charmm27.ff/forcefield.itp"??? ??? ??? parameter??? ?? ??? ???? ?? itp ??? include?? ????. #include? c ????? #include? ??? ?? ???, ? line? GROMACS ??? ??? charmm27 force field parameter?? ?? top file? ?????? ????. ??? ? ?? section?? ?? system? ????.[ system ]; NameProtein[ molecules ]; Compound #molsProtein 1System? ??? molecule? ???? Protein?? 1?? Protein molecule? ???? ??. ? ? section? ?? genbox? ?? solvent molecule? system? ???? ????.5-2. ??(vacuum) ???? ?????MD ????????? ?? ?? ???? ?? ???? ???? ?????? ???? ?? ??? energy minimization? ? ??? ??. ?? force field? ?????? ??? system? ??? ??? ???? ?? ???? local strain? ?? ?? production? ?? ?????? ??? ? ?? ?? ????. Energy minimization? ???? mdrun ????? ?? ?? ?? steepest descent algorithm? ???? ???. ?? input ??? tpr ??? ???? ??. minimize.mdp ?? ??? ??? ???? vi editor? ?? ??.gmx grompp -f minimize.mdp -c 2ECH_mod.gro -p 2ECH_ -o 2ECH_min.tpr? ??? ??. ??? ????? error message? ?????, ?? system? ?? box? ??? cutoff length? ?? ?? ??? ???? ???. Box? ??? gro ??? ? ??? ?? ???? ??. gro ??? ?? ? ??? 10.0 ??? ??? ?? ???? ???? ????? ??? ???? ??. tpr ??? ??? ?????? ??? ??.mdrun ????? ?? energy minimization? ? ??.gmx mdrun -s 2ECH_min.tpr -c 2ECH_min.gro -e 2ECH_min.edr??? ??? ?? ? ???? ?? output ???? ????. ??? gro ??? energy minimization? ??? ? system? ????. vmd? ?? visualization ????? ???? minimization? ?? ?? ?? ??? ???? ?? ????.Minimization? ???? gro ?? ??? edr ??? trr ??? ?????, ???? ?? system? energy? trajectory(coordinate + velocity)? ????. ? ???? binary??? ???? ?? ? ??, energy?? ????? ???? ??? ?? ? ?? ASCII data? ???? ??. ?? ??? ?? ??????? ??? data?? analysis? ??? ? ??. ?? edr ??? ?? ??? ??? ???.gmx energy -f 2ECH_min.edr -dp -o 2ECH_min.xvg? ???? ???? ?? ??? ??? ??? data? ????? ??? ?? ???, ‘Potential’ ? ???? ????? edr ???? potential energy ??? ???? 2ECH_min.xvg? ????. vi ???? ???? ??? header ??? ???, x?? step, y?? potential energy? plot?? energy minimization? ?? ?? ??? ??? ??.?? MD ?????? ??? ????. Energy minimization? ? ??? ?? parameter? ?? ??. md.mdp? ?? minimize.mdp? ??? ? ?, grompp? ???? tpr ??? ???.gmx grompp -f md.mdp -c 2ECH_min.gro -p 2ECH_ -o 2ECH_md.tpr??? ?? ??. ??? connectivity? ??? ????? top ??? ?? ???? ??? ??? ???? ???, gro ??? minimization? ?? ??? ?? ???? ??. ?? ??? ?????gmx mdrun -s 2ECH_md.tpr -c 2ECH_md.gro -e 2ECH_md.edr? ???? md ?????? ? ? ??. ????? ???? ??? edr ??? energy? ???? ???? total energy? ??? ?? plot??. ????? ?? ???? thermostat? ?? ???? system? ????, ???? ???? ?? ??? ??.????? ?????? ?? ?? ??? ?????. ??? ????? solvation? ?? ?? ??? ?? ??? ??? ?????? MD? ???? ??. ? ?? solvent effect? ??? ??? ??. Solvent? ??? ?????? ?? ?? ?? ??? ??? dielectric screening coefficient? ???? ???. ?? dielectric coefficient? ? 80??? mdp ??? epsilon_r = 80??? ??? ???? ?? ?????? ??? ? ??. ?? ?? ??? ??? ?? ???? ????? ??? ??? ?? ???, ??? ?? ?? ???? ?? ?? ???.5-3. Periodic Boundary Condition? ??? ??????? ?????MD ?????? ?? ???? ?? ???? ??? system?? ????? ?????? ????? ??. ???? ?? ? ?? ??? ??. 5-2?? ??? ?????? dielectric? ???? ??? ???? implicit solvent ???, ??? ? ??? system ??? ??? ? ?????? ?? explicit solvent ??? ??. ??? explicit solvent model? ??? ??? ??? ????? ? ??? ?? ?????? ? ? ???, ? ??? ???? ???? ??. ? ???? periodic boundary condition? ??? system? ?? ???? ??? box? ? ???? ???, ? ???? MD ?????? ? ? ???.5-2??? ???? minimized geometry? ?? gro ??? ? ??? solvation?? ??. ? ?? genbox ?? ???? ????.gmx solvate -cp 2ECH_min.gro -cs spc216.gro -o 2ECH_solv.gro -p 2ECH_??? -cp? ??, ? system? ??? ?? ???? -cs? ??? ??? ?? ????. ??? tip3p water model? ????? spc216 water model? gro ??? ??? ???. ??? ?? ?? ??? tip3p? spc216? ?? 3-site model?? ??? model? ??? ??? ?? ??? ?? ?? ?? equilibration? ?? ??? ? ?? ????. ?? ? ??? 4-site model? tip4p model?? ?? ?? model? ????? ?? ?? gro ??? ??? ??? ? ???. ?? ???? ??? gro ???? GROMACS? ??? directory? /share/gromacs/top? ?? ??.?? top ??? ?? ???? [ system ]? [ molecule ] ??? ?????. ??? ??? ??? genbox? ??? solvent? ???? ?? ?? ??? ? ??. ?? vmd? ??? 2ECH_solv.gro? ?? ??, ?????? solvent box? ??? ?? ??? ? ??. ??? system? solvent box? ?? ???? ?? ??? ???? box ??? ???? ?? ???. ?? ??? ???? ???? editconf ????? ????. ? ????? system? center of mass? box ??? ??? ??? ??????, ?? ? ????? ? ? ?? ? ??. Box? 10nm ??? ??????? -center 5 5 5?? ??? ???? system? center of mass? box? ???? ?? ?? ? ??.gmx editconf -f 2ECH_min.gro -o 2ECH_min_center.gro -center 5 5 5?? 2ECH_min_center.gro? ?? solvation?? ??. ? ?? ? ?? ? ??? ?? solvent ??? ??? ??. ??, ??? ??? #.1#? ???? ??.gmx solvate -cp 2ECH_min_center.gro -cs spc216.gro -o 2ECH_solv.gro -p 2ECH_??? 2ECH_solv.gro? vmd? ?? system? box ??? ? ???? ??? ??.?? minimize? ?? md ?????? ??? ????. tpr ??? ??? ?????? ?? ?? ???? ??? ???? ? ? ??.gmx grompp -f minimize.mdp -c 2ECH_solv.gro -p 2ECH_ -o 2ECH_solv_min.tprgmx mdrun -s 2ECH_solv_min.tpr -c 2ECH_solv_min.grogmx grompp -f md.mdp -c 2ECH_solv_min.gro -p 2ECH_ -o 2ECH_solv_md.tprgmx mdrun -s 2ECH_solv_md.tpr -c 2ECH_solv_md.gro -e 2ECH_solv_md.edr -o 2ECH_solv_md.trr??? ? command? copy?? ???? ????, ? ????? output? ?? ??? input?? ???? ??? ? ??? ????? ?? ??. ??? ?? ??? ?????, ??? ???? ??? 6?? ??? ?? ????? ??.md ??????? ??? trajectory? 2ECH_solv_md.trr? trjconv? ???? gro ??? ??? ?? vmd? ?? ?? system? ???? ??? ????? ??? ? ??.5-4. ????? ??? ?????? ??? ?? ?? ???? ?? ?? ?? ?? ?? ???? ???? ??? ??? ??? ??? ??? ??? ???. ??? ??? ??? ???? protein? radius of gyration? ???? ?? ?? ???? ???? ?? ??? ?? ???, solvation free energy? ???? ensemble level?? ligand-protein ?? ???? ????? ???? ?? ?? ?? ?? ?? ?? ? ? ???, ?? ??? ??~??? ?? ??? ??? ??? ??/???? ???? ?? ? ?? ????? ??? MD ?????? ????.6. Force FieldForce field? MD ?????? ?? ?? parameter? ?????. ? bonded interaction? non-bonded interaction? ???? ??? model??? ? ?? ??. ?? system??? ?????? ??? force field? ???? ??? ?????? ??. GROMACS??? 20? ?? ?? force field? ?? ?????, ??? ???? ???? ??? ?? ??. ???? force field? ??? ??, ?? ??? MD ?????? ???? ??? ? ??.California State Univ.? Eric J. Sorin ??? AMBER?? MD ????? force field? GROMACS??? ?? ??? ? ??? ?? ??. ?? ??? ?????, GROMACS? ??? directory ?? /share/gromacs/top ? ?? ??? ??, ffamber03??? directory? ?? ??? ???.??? ???? ?? ??? ??? ???.rtp - residue database. Amino acid? nucleic acid?? ?? ????? connectivity? ?? ??.itp - interaction database. Bonded/nonbonded interaction?? ?? ??.hdb - hydrogen database. pdb ??? ??? ?? ?? ??? ??? ????? ?? ??.tdb - termini database. Terminal residue? ??? ????? ?? ????? ?? ??? GROMACS? ?? ??? force field? ??? ??? ???? ???. ?? ???? ??, directory? ??? .ff? ??? ?? ??, ffamber03 directory ??? forcefield.doc? forcefield.itp?? ? ?? ??? ??? ??. ffamber03 directory? ?? ?? .ff? ?? ffamber03.ff? ???, vi editor? forcefield.doc? ?? ??? ??? ?? Force Field? ??? ??? ?? ???. ??? ffamber03.itp?? ??? ??? forcefield.itp? ?? ?? ??.?? pdb2gmx? top ??? gro ??? ??? ??. ??? ?? ??? force field? ??? ?? ??? ? ?? ???. ??? ? force field? ???? error? ??? ???. Error message? ? ?? ??, ?? ??? ??? ??? ?? ????? error? ??? ???? ??? ??? ??.- ? ?? ??? error?, ffamber03 Force Field? N-terminal? C-terminal ??? ??? ?? ??? ?? ????. ?? ffamber03? terminal residue? ?? ???? ?? ??? ???, pdb ???? ?? residue? terminal??? ???? ?? ?? ??? ??? ???? ??. pdb ??? ?? 1? residue? GLU? 49? residue? THR? ?? ???? ?? ??? ???, ???? ???? ffamber03.ff directory ?? ffamber03.rtp? ?? ??? ??.- ? error? ???, Lysine? ???? LYS?? residue? rtp database? ???? ???? error? ???. ffamber03?? Lysine? ???? residue type? LYS? ???, protonation state? ???? ?? ? ??? ???? (LYN, LYP). ? residue type ? pdb ??? ??? ???? ?? ???? rtp file? pdb file? ???? ??? ??.- ?? error? Histidine? ???? HSE?? residue? ?? ???. Histidine? ???? ? ?? ?? protonation state? ???? 3?? residue type? ??. ????? pdb ??? ???? ?? ??.- ?? residue 4? Serine? HG1 atom? rtp ??? ???? ???? error? ???? ??. rtp ??? ??? ?? pdb ??? HG1? rtp ??? atom name? ?? ??? ??.- ??? error? ?? ?????, rtp ???? C-terminal? Threonine? ??? ?? ??, atom OC1? O?, OC2? OXT? ?????? ??? ? ??.??? force field? ???? ????? ???? ?? ??? ?? error?? ??? ? ??, ??? ??? ???? ??? ?? ??? ??? ?? ????? ?? ??. ?? ?? top file? gro file? ??? ? ????? ?? ?? ????.7. ?? 3 - Coumarin 153 ?? ??? solvent response function ??(?? ??: J. Chem. Phys. 135, 014107 (2011))? ???? ?? ??? Coumarin 153? ?? ??? ?? ?? force field? ????, ??? ?? ??? ??? ?? relaxation process? ?? ?? solvent response function? ?? ???.7-1. ??? ??Stokes shift? ?? ??? absorption maximum? fluorescence maximum? ??? ????. ?? ??? ?? ??? ?? ??? ??? ?? (potential energy surface) ??? ???, ?? ??? ??? ???. ??? ?? ??? ?? ???? ?? ?? ??? ??? ??? ?? ??? ???? ?? ??? ??? ?? ?? ??? ????? ??????, ? ?? ??? ??? ?? ???? ???? ?? ?? ???? ??? ?? ??? ??? ???? ???. ?? ??? ??? ??? ?? ?? ?? ?? ??? ?????, ??? ?? ??? ???? ????? (Franck-Condon approximation) Stokes shift? ?? ???. ??? fluorescence? nanosecond ??? ??? ? ????? ???? ????, ? ??? ?? ???? ???? relaxation? ????? ????. ??? Stokes shift? ?? ??? ??? ?? ?? ???? ??? ? ??? ??? ? ??? ???? ??. ?? Stokes shift? ?? long-time limit??? ?? ????, ? ??? ???? ???.?? 4. Rhodamine 6G? Stokes shift(??: Wikipedia)??? ?? Stokes shift? ??? dynamic Stokes shift? ???, ??? ?? ????.?? ?? <> ? ensemble average? ????. ?? normalize ?? ???? 1? ?? ?? solvent response function?? ??.Solvent response function? time-resolved pump-probe experiment ?? ??? ????? ??? ? ??. ?????? ?? ? ?? ??? ?? ???, ??? ??? ?? ???? ?? ?? ??? ?? ??? ???? force field? ???? ????? ??.7-2. MD ?????? ?? solvent response function? ??coumarin ??? ??? sample.gro ??? vmd? ???? ?? ?? methanol ?? ??? ??? solvation ?? ?? Coumarin 153 ??? ? ? ??. ?? 300K, 1?? ??? 1 ns equilibration ? 1 ns production run? ????, production ???? 10 ps?? frame? ??? ???? ensemble ?? ?? ?? 100?? gro file???. excited state? ???? force field?? excited_? excited_ ? ?? ??? ??. ??? coumarin molecule? ???? ???? ??? ?? ???, ??? ??/?? ??? ? bonded interaction parameter??? excited state? ?? ?? ??? ? ???.?? ??? gro file? ???? ??? ??? ?? ??? ?? 2 ps ??? solvent response function? ?? ??. ? ?? gro file? COU001.gro? ???? ????.- ??, ?? ???? excited state? ??? ??? ???? ?? excited_? COU001.gro? ???? 2 ps ?????? ???. mdp ??? excited.mdp? ????. trr ??? edr ??? ??? COU001.trr? COU001_e.edr ? ????. ? ?????? ?? 5 fs?? system? ???? ??? ???? ????.- ? ?? ???? ??? ??? snapshot?? ??? excitation energy? ??? ?? ?? ? ??? ???, ??? ???? excited state? ?????? ??? ground state? ???? ???? ??. ? ???? system? ?? ? geometry?? COU001.trr ? ???? ??? ????. tpr ??? ??? ? ??? ? ground.mdp ? ????, MD ????? ???? -rerun COU001.trr ?? ??? ??? ?? ????? COU001.trr ? ??? snapshot?? ????? ground state energy ?? ???? ??. trr ??? edr ??? ??? COU001_rerun.trr ? COU001_g.edr ? ????. COU001_rerun.trr? ??? ?? ?????? ?????? ?? ? ??? ??? ??.- ?? COU001_g.edr ? COU001_e.edr ??? energy gap? ??? ?? ??? ?? ? ??. ?? ??? ??? ???? ???? ?? ??? ??.- 100?? gro file? ?? ? ??? ?? ???? ???? ???? ? ???. ? ???? -26.8630 kJ/mol ? ????. ?? ?? ?? ??? ? ?? ??? ???? ???? shell script? ??? ?? ??? ??. srf_charge directory ??? ???? run_srf.sh ? ??? ??? ???? ??? ??. ?? ??? ??? ???? ??? ?? ??? ???? ??? ?? ??? ?? ??? ?? ???? ?? ??? ????? ?? ??? ???? ?? ??? ????.- ?? ??? ??? ? ??? excited state model? excited_ ? ???? ? ??? ??? ? ?? ??. srf_full ??? ??? directory? ??? ?? ???? script file? ????. ????? topology file? ????, ??? ?? csh script? ???? ??? ?? ????. ? ?? ? ?? -363.8034 kJ/mol ??.- ????? ??? ? ?? ? ????. Charge? ???? ??? bonded interaction parameter?? ???? ??? ?? ? ??? ????? ?? ??? force field? ??? ???? ??? ??. ................
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