MD EXPERIMENT. Initialization : Relaxation : Equilibration : Productive run: Analysis : building molecular system; initial coordinates

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1 MD EXPERIMENT Initialization : Relaxation : building molecular system; initial coordinates the system is brought to a state where actual Equilibration : Productive run: Analysis : dynamics can be performed to ensure the system is equilibrated data (trajectory) is accumulated the simulation data are converted to meaningful information

2 INITIALIZATION ( building molecular system; initial coordinates ) RTF residue topology file PARA build parameter file script PSF protein structure file CRD / PDB CRD / PDB coordinate file coordinate file

3 The RESIDUE TOPOLOGY FILE contains definitions of the molecular building blocks (residues) which are used to build large molecular systems: the name of each atom type in the parameter set the mass of each atom type atom s partial charge in a particular residue the covalent structure for each residue the internal coordinates for each residue The PARAMETER FILE is associated with the RTF file and it contains all the necessary parameters for calculating the energy of the molecular system: the equilibrium bond distances and angles the force constants Lennard-Jones 6-12 potential parameters These parameters are associated with particular atom types

4 CHARM_22 parameter set: type mass chemical in potential type 1 C C! carbonyl C, peptide backbone 2 CA C! aromatic C 3 CT C! aliphatic sp3 C for CH 4 CT C! aliphatic sp3 C for CH2 5 CT C! aliphatic sp3 C for CH3 6 CPH C! his CG and CD2 carbons 7 CPH C! his CE1 carbon 8 CPT C! trp C between rings 9 CY C! TRP C in pyrrole ring 10 CP C! tetrahedral C (proline CA) 11 CP C! tetrahedral C (proline CB/CG) 12 CP C! tetrahedral C (proline CD) 13 CC C! carbonyl C, asn,asp,gln,glu,cter,ct2 14 CD C! carbonyl C, pres aspp,glup,ct1 15 CPA C! heme alpha-c 16 CPB C! heme beta-c 17 CPM C! heme meso-c 18 CM C! heme CO carbon 19 CS C! thiolate carbon 20 CE C! for alkene; RHC=CR 21 CE C! for alkene; H2C=CR

5 * TIPS4P WATER + ACETON + XENON * PARAMETER FILE * BOND HT OT HT HT LP OT CA CT CA OA CT HA ANGLE HT OT HT OA CA CT CT CA CT CA CT HA HA CT HA NONBONDED GROUP CDIEL SWITCH - VGROUP VSWITCH - CUTNB 10.0 CTOFNB 8.0 CTONNB EPS 1.0 E14FAC 0.4 HT ! Water H OT ! Water O LP ! lone pair CA ! Carbonyl C CT ! Aliphatic sp3 C OA ! Carbonyl O HA ! nonpolar H XE ! xenon DIHEDRAL OA CA CT HA HA CT CA CT IMPROPER CA CT CT OA !

6 TIPS4P + ACETON + XENON * TOPOLOGY FILE * MASS 1 HA MASS 2 CA MASS 3 CT MASS 4 OA MASS 5 HT MASS 6 OT MASS 7 LP MASS 8 XE AUTOGENERATE ANGLES DIHEDRAL RESI TIP4! TIPS4P WATER MODEL GROUP ATOM OH2 OT 0.00 ATOM OM LP ATOM H1 HT 0.52 ATOM H2 HT 0.52 BOND OH2 H1 OH2 OM OH2 H2 H1 H2 THET H1 OH2 H2 PATCH FIRS NONE LAST NONE RESI XENN! XENON ATOM RESI ACTN GROUP ATOM C CA 0.52 ATOM O OA GROUP ATOM CT1 CT ATOM HZ1 HA 0.09 ATOM HZ2 HA 0.09 ATOM HZ3 HA 0.09 GROUP ATOM CT2 CT ATOM HZ4 HA ATOM HZ5 HA ATOM HZ6 HA BOND O C BOND C CT1 BOND C CT2 BOND CT1 HZ1 BOND CT1 HZ2 BOND CT1 HZ3 BOND CT2 HZ4 BOND CT2 HZ5 BOND CT2 HZ6 IMPR C CT1 CT2 O GROUP ATOM XE XE 0.0 HZ1 CT1 ---HZ2 / / HZ3 O---C \ HZ4 \ CT2--_HZ5 HZ6

7 RESI ALA GROUP ATOM NN N1-0.47! ATOM HN H 0.31! HN-N ATOM CA CT1 0.07! HB1 ATOM HA HB 0.09! / GROUP! HA-CA--CB-HB2 ATOM CB CT3-0.27! \ ATOM HB1 HA 0.09! HB3 ATOM HB2 HA 0.09! O=C ATOM HB3 HA 0.09! GROUP ATOM C C 0.51 ATOM O O BOND CB CA N HN N CA BOND C CA C +N CA HA CB HB1 CB HB2 CB HB3 DOUBLE O C IMPR N -C CA HN C CA +N O DONOR HN N ACCEPTOR O C IC -C CA *N HN IC -C N CA C IC N CA C +N IC +N CA *C O IC CA C +N +CA IC N C *CA CB IC N C *CA HA IC C CA CB HB IC HB1 CA *CB HB IC HB1 CA *CB HB

8 CRD file: PDB file:... ATOM 82 N CYS ATOM 83 CA CYS ATOM 84 C CYS ATOM 85 O CYS ATOM 86 CB CYS ATOM 87 SG CYS ATOM 88 H CYS ATOM 89 HA CYS ATOM 90 1HB CYS ATOM 91 2HB CYS ATOM 92 QB CYS ATOM 93 N LEU ATOM 94 CA LEU ATOM 95 C LEU ATOM 96 O LEU ATOM 97 CB LEU * methanol * METN CB METN OG METN HG METN HB METN HB METN HB

9 Generate PSF and initial coordinates!read in Topology and Parameter files OPEN UNIT 1 READ FORM NAME acxt4p.rtf READ RTF CARD UNIT 1 OPEN UNIT 1 READ FORM NAME acxt4p.prm READ PARAM CARD UNIT 1!generate 768 water and 1 aceton molecules READ SEQUENCE TIP4 768 GENERATE ICE NOANGLES NODIHEDRALS READ SEQUENCE CARD * aceton molecule * 1 ACTN GENERATE MAIN FIRST NONE LAST NONE!read in coordinates OPEN UNIT 1 READ FORM NAME ice768a1.crd READ COOR CARD UNIT 1! Adjust the bonds SHAKE BONH FAST PARAM TOL 1.0E-12!build coordinates for the loan pairs LONE BISE DIST 0.15 ANGLE 0.0 DIHE SELE ATOM ICE * OM END - SELE ATOM ICE * OH2 END - SELE ATOM ICE * H1 END - SELE ATOM ICE * H2 END COOR SHAKE!write out the coordinates in charmm format OPEN UNIT 1 WRITE FORM NAME i4_768a1.crd WRITE COOR CARD UNIT 1!write out the PSF OPEN UNIT 1 WRITE FORM NAME ic768a1.psf WRITE PSF CARD UNIT 1

10 * Generate PSF and CHARMM * coordinate set *! Read in Topology and Parameter files open unit 1 card read name top_all22_prot.inp read RTF card unit 1 open unit 1 card read name par_all22_prot.inp read PARA card unit 1! Read sequence from the PDB coordinate file open unit 1 card read name 1mbo.pdb read sequ pdb unit 1!generate the PSF and also the IC table generate prot setu! read in pdb coordinate file! build in hydrogens if using a crystal structure hbuild sele all end! build in missing coordinates using values in the topology file ic fill ic build! write out the protein structure file (psf) and! the coordinate file in pdb format. open write formatted unit 2 name 1mbo.psf write psf card unit 2 open unit 1 card write name 1mbo_h.pdb write coor pdb unit 1 stop open unit 1 card read name 1mbo.pdb read coor pdb unit 1

11 PSF file for aceton 2!NTITLE * ACETON MOLECULE * DATE: 10/25/ 2 9:43:41 CREATED BY USER: lemak 10!NATOM 1 MAIN 1 ACTN C MAIN 1 ACTN O MAIN 1 ACTN CT MAIN 1 ACTN HZ E MAIN 1 ACTN HZ E MAIN 1 ACTN HZ E MAIN 1 ACTN CT E MAIN 1 ACTN HZ E MAIN 1 ACTN HZ E MAIN 1 ACTN HZ E !NBOND: bonds

12 15!NTHETA: angles !NPHI: dihedrals !NIMPHI: impropers !NDON: donors 0!NACC: acceptors 0!NNB !NGRP NST

13 MINIMIZATION & HEATING ( relaxing & equilibrating molecular system) RTF residue topology file PARA CHARMM parameter file script PSF structural file CRD / PDB starting coordinates CRD / PDB initial coordinates

14 * minimized coordinates *! Read in Topology and Parameter files open unit 1 card read name top_all22_prot.inp read RTF card unit 1 open unit 1 card read name par_all22_prot.inp read PARA card unit 1! Read in PSF and Coordinate file open read formatted unit 1 name 1mbo.psf read psf card unit 1 open read formatted unit 3 name 1mbo_h.pdb read coor pdb unit 3! non bonded interaction nbond cutnb 15.0 ctonnb 14.0 cofnb 14.5 switch vswitch cdiele epsilon 1.0! minimize initial structure energy mini sd nsteps 500 nprint 50 energy open write formatted unit 2 name 1mbo_min.pdb write coor pdb unit 2 stop

15 * heating and equilibration *! Read in Topology and Parameter files open unit 1 card read name top_all22_prot.inp read RTF card unit 1 open unit 1 card read name par_all22_prot.inp read PARA card unit 1! Read in PSF and Coordinate file open read formatted unit 1 name 1mbo.psf read psf card unit 1 open read formatted unit 3 name 1mbo_min.pdb read coor pdb unit 3! non bonded interaction bbond cutnb 15.0 ctonnb 14.0 cofnb 14.5 switch vswitch cdiele epsilon 1.0! heating run open write formatted unit 31 name 1mbo_hit.res dyna leap verlet start nstep 6000 timestep iseed firstt 0 finalt ihtfrq 10 teminc.5 ieqfrq 0 iasors 1 iasvel 1 isvfrq 500 iprfrq 500 nprint iunrea -1 iunwri 31 iuncrd -1 imgfrq 10 inbfrq 10! equilibration run open write formatted unit 32 name 1mbo_hit.res open write formatted unit 31 name 1mbo_eqv.res dyna leap verlet restart nstep 6000 timestep isvfrq 500 iprfrq 500 nprint ieqfrq 50 iasors 0 iscvel 0 iasvel 1 ichecw 1 twindh 5.0 twindl -5.0 iunrea 32 - iunwri 31 iuncrd -1 imgfrq 10 inbfrq 10! write out coordinates open write unit 2 card name 1mbo_eqv.pdb write coor pdb unit 2 stop

16 PRODUCTIVE RUN ( accumulating trajectory; last coordinates ) RTF residue topology file PARA CHARMM parameter file script trajectory file (binary format) PSF structural file CRD / PDB starting coordinates CRD / PDB last coordinates

17 * productive run *! Read in Topology and Parameter files open unit 1 card read name top_all22_prot.inp read RTF card unit 1 open unit 1 card read name par_all22_prot.inp read PARA card unit 1! Read in PSF and Coordinate file open read formatted unit 1 name 1mbo.psf read psf card unit 1 open read formatted unit 3 name 1mbo_min.pdb read coor pdb unit 3! non bonded interaction bbond cutnb 15.0 ctonnb 14.0 cofnb 14.5 switch vswitch cdiele epsilon 1.0! productive run open write formatted unit 31 name 1mbo_last.res open write formatted unit 30 name 1mbo_eqv.res open write unit 30 name 1mbo_eqv.bin dyna leap verlet restart nstep timestep isvfrq 500 iprfrq 500 nprint ieqfrq 0 finalt 300 iunrea 30 iunwri 31 nsavc 100 iuncrd 30 inbfrq 10! write out coordinates open write unit 2 card name 1mbo_last.pdb write coor pdb unit 2 stop

18 * 6 aceton molecules * on ice surface * OPEN UNIT 1 READ FORM NAME acxt4p.rtf READ RTF CARD UNIT 1 OPEN UNIT 1 READ FORM NAME acxt4p.prm READ PARAM CARD UNIT 1 READ SEQUENCE TIP3 768 GENERATE ICE NOANGLES NODIHEDRALS OPEN UNIT 1 READ FORM NAME ice768a6s.crd READ COOR CARD UNIT 1 SHAKE BONH FAST PARAM TOL 1.0E-12 LONE BISE DIST 0.15 ANGLE 0.0 DIHE SELE ATOM ICE * OM END SELE ATOM ICE * OH2 END - SELE ATOM ICE * H1 END SELE ATOM ICE * H2 END COOR SHAKE READ SEQUENCE CARD * 6 aceton molecules * 6 ACTN ACTN ACTN ACTN ACTN ACTN GENERATE MAIN FIRST NONE LAST NONE OPEN UNIT 1 WRITE FORM NAME i768a6.psf WRITE PSF CARD UNIT 1

19 ! Read in Image Transformation file SET SET SET OPEN UNIT 1 READ FORM NAME surf.img READ IMAGE CARD UNIT 1! Set up NB lists UPDATE GROUP FSWITCH CDIE EPS 1.0 VGROUP VSWITCH VDIS CUTNB 14.0 CTOFNB 12.0 CTONNB 10.0 CUTIM ! Froze 4 water bilayers CONS FIX SELE BYNU 1 : 1536 END! Turn on fixation of H- bonds SHAKE BONH FAST PARAM TOL 1.0E-12! dynamics run OPEN UNIT 21 WRITE CARD NAME ia6_130.rst OPEN UNIT 30 WRITE CARD NAME ia6_130e.dat OPEN UNIT 31 WRITE UNFORM NAME ia6_130t.bin DYNA LEAP VERL STRT NSTEP TIMESTP INBFRQ -1 IHBFRQ 0 IMGFRQ -1 - PRINT 100 NSAVC 100 ISVFRQ 1000 IPRFRQ 1000 NSAVV 0 - KUNIT 30 IUNCRD 31 IUNWRI 21 IUNREA -1 IUNVEL -1 - IHTFRQ 0 IEQFRQ 0 NTRFRQ 0 IASORS 0 IASVEL 1 - ISCVEL 0 ICHECW 0 TWINDH 0 TWINDL 0 TEMINC 0 - TCONST TCOUPL 0.5 TREF FIRSTT FINALT 130.0! Write out the last coordinates in charmm format OPEN UNIT 1 WRITE FORM NAME ia_130.lst WRITE COOR CARD UNIT 1 * IMAGE FILE FOR 2D RECTANG. TRANSFORMATION *BOX @8 IMAGE X TRANS IMAGE A TRANS IMAGE XY TRANS IMAGE Y TRANS IMAGE AY TRANS IMAGE XB TRANS IMAGE B TRANS IMAGE AB TRANS END

20 ANALYSIS OF MD TRAJECTORY 1. Mean energy (energy components) = >= < M i t i E M E 1 ) ( 1 2. Conformational properties Radius of gyration: R.M.S. fluctuations: = = = N a m c a a N a a G r r m m R ) ( 1 ( ) 2 1/ ) ) ( ( 1 1 = = = M i averg a i N a a r t r N M σ

21 ANALYSIS RTF residue topology file PARA CHARMM parameter file script trajectory file (ASCI format) PSF structural file trajectory file (binary format) energetic characteristics

22 * aceton molecule on ice surface Trajectory analysis! Read in Topology and Parameter files OPEN UNIT 1 READ FORM NAME acxm.rtf READ RTF CARD UNIT 1 OPEN UNIT 1 READ FORM NAME acxm.prm READ PARAM CARD UNIT 1! Read in the RTF and coordinates OPEN UNIT 1 READ FORM NAME i768a1.psf READ PSF CARD UNIT 1 OPEN UNIT 1 READ FORM NAME i768a1.crd READ COOR CARD UNIT 1! Read in Image Transformation file SET SET SET OPEN UNIT 1 READ FORM NAME surf.img READ IMAGE CARD UNIT 1 UPDATE GROUP FSWITCH CDIE EPS VGROUP VSWITCH CUTNB CTOFNB 12.0 CTONNB 10.0 CUTIM !trajectory file OPEN UNIT 30 READ UNFORM NAME ia1.bin TRAJECTORY QUERy UNIT 30 OPEN UNIT 31 WRITE FORM NAME e_tot.dat OPEN UNIT 32 WRITE FORM NAME e_int.dat SET 1 1 LABEL LOOP! Read in next coordinate set TRAJ READ! Update NB lists UPDATE GROUP FSWITCH CDIE EPS 1.0 VGROUP - VSWITCH VDIS CUTNB 14.0 CTOFNB CTONNB 10.0 CUTIM ! Calculate total energy and write it out GETE PRINT UNIT 31! Calculate interaction energy and write it out INTER SELE BYNUM 1 : 3072 END - SELE BYNUM 3073 : 3078 END UNIT 32 INCR 1 BY 1 IF 1 LT?NFILE GOTO LOOP STOP

This Answer/Solution Example is taken from a student s actual homework report. I thank him for permission to use it here. JG

This Answer/Solution Example is taken from a student s actual homework report. I thank him for permission to use it here. JG Chem 8021 Spring 2005 Project II Calculation of Self-Diffusion Coeffecient of