1 / 32

Clase 6: Detalles de la simulación

Clase 6: Detalles de la simulación. SANDER. NMR, X-Ray,. QM, crystal data, experiments,. nucgen. Estructura. Parámetros. ( Construcción de ác. nucléicos ). resp. Antechamber. ( Ajuste de cargas electrostáticas ). ( Set-up automatizado ). LEaP. coordinate_file. topology_file. nmode.

aerona
Download Presentation

Clase 6: Detalles de la simulación

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript


  1. Clase 6: Detalles de la simulación

  2. SANDER

  3. NMR, X-Ray,... QM, crystal data, experiments,... nucgen Estructura Parámetros ( Construcción de ác. nucléicos ) resp Antechamber ( Ajuste de cargas electrostáticas ) ( Set-up automatizado ) LEaP coordinate_file topology_file nmode Obtención de datos útiles en NMR ( Análisis de modos normales ) LES sander gibbs intense profec ( Estrategia especial de aumento de sampling conformaciona en MD ) ( Dinámica molecular) ( Cálculo de diferencias de energía libre ) spectrum ( Genera grids de reactividad basadas en energía libre ) fantasian Programas de análisis ptraj carnal anal MM-PBSA ( Análisis de energías ) ( Cálculo de energías libres ) ( Procesado de trayectorias )

  4. NMR, X-Ray,... QM, crystal data, experiments,... Estructura Parámetros LEaP coordinate_file topology_file SANDER ( Dinámica molecular) Programas de análisis ptraj carnal anal MM-PBSA ( Análisis de energías ) ( Cálculo de energías libres ) ( Procesado de trayectorias )

  5. Descripción general simulación • TIMLIM: Tiempo límite CPU simulación • IMIN: Decisión tipo cálculo • 0: Dinámica • 1: Minimización • NMROPT: Flag NMR • 0: No NMR restrains • >0: NMR restrains/weight changes • 2: NOESY volume restraints or chemical shifts restrains

  6. Nature & Format of the input • NTX: Read coordinates, velocities and box • 1: X formatted no V • 5: X and V are read formatted • 7: X,V and Box are read formatted • IREST: Flag to restart the run: • 0 No • 1 Restart (need X, V) • NTRX: Format for restraint from file refc • 0 unformatted • 1 formatted

  7. Nature & Format of the output • NTX0: Format for coordinates velocities and box • 1: X formatted • 0: unformatted • NTPR: Every NTPR mdifo will be printed. • NTWR: Every NTWR restart file will be written. • IWRAP: 1 Center solute in the primary box.

  8. Nature & Format of the output • NTWX, NTWV, NTWE: frequency of the output of coordinates, velocities, energies (If .ne. 0) • NTWXM, NTWVM, NTWEM: If .ne. 0 limits the output of coordinates, velocities, energies • NTWPRT: archive limit flag (V,X) • 0 all atoms • <0 only solute • >0 only atoms 1NTWPRT

  9. Potential function • NTF Force evaluation • 1: complete interaction • 2: bonds involving H are omitted • 3: all the bonds are omitted • ... • NTB Periodic boundary conditions • 0: No periodicity • 1: Constant volume • 2: Constant pressure

  10. Periodic Boundary Conditions(PBC)

  11. Potential function • DIELC: multiplicative factor for dielectric constant default 1.0. See options in GB/SA • CUT: Cutoff for non-bonded interactions. See Ewald • SCNB: Scaling of 1-4 vW interactions (1/SCNB). Default 2 • SCEE: Scaling of 1-4 electrostatic (1/SCEE). Default 1.2

  12. Potential functionGB calculations • IGB: Use of generalized Born model (GB) IGB=0 no GB, IGB=1. (GB/SA), IGB=2 (vacuum calculation), IGB=3 (dist. dep. dielc const.) • GBPARM: 1 (Beveridge), 2 (Case) Two sets of GB parameters • READRAD: if .ne.0 read vW radii for GB calculations • OFFSET: fine tune of Born radii defaults 0.09 or 0 • IGBFREQ: Frequency of update of Born radii • GBSA: If .eq.1 SA corrections to GB. • SURFTEN: Use non-default surface tension.

  13. Generalized Born Método de introducir solvente continuo Técnica potente pero poco contrastada No recomendada para no expertos

  14. Potential functionPolarizable potentials • IPOL. Inclusion of polarization • 0 No polarization • 1 Use polarization • 2 Use polarization + 3 body interactions No recomendado para no expertos

  15. Potential functionFrozen/restrained atoms • IBELLY: • 0 normal run • 1 Belly run. Only a set of atoms (specified later) are allowed to move • NTR: Restraints in the Cartesian space (use harmonic restraints) • 0 No restraints • 1 MD with restraints on specific atoms

  16. Energy minimization • MAXCYC: Maximum number of cycles. • NCYC: After NCYC change from one method of optimization to other. • NTMIN: Method for minimization • 0 Conjugate gradient • 1 For NCYC steepest descent then CG • 2 Only steepest descent • DX0, DXM, DRMS: Details of minimization procedure: Use defaults

  17. Molecular dynamics • NSTLIM: Number of MD-steps per NRUN to be performed • NDFMIN: Number degrees of freedom to remove. If NTCM or NSCM.ne.0 use 6, otherwise 0. • NTCM: • 0 Do not remove translational/rotational moves around center of mass • 1 Remove at the beginning • NSCM: Remove translational/rotational moves around center of mass every NSCN steps (def 0) • T: Time at the start, default 0.0 • DT: Integration time

  18. Etapa de integración • Si no constraints en ningún enlace 0.0005 ps. • Si constraints (SHAKE) en enlaces X-H 0.001 ps • Si constraints en todos los enlaces 0.002 • Si el sistema esta muy tensionado, T o P es elevada usar 0.001 ps • Reducir la etapa de integración aumenta linealmente el costo de la simulación pero puede ser necesario para evitar discontinuidades

  19. Regulación de la temperatura • TEMP0: Reference temperature • TEMPI: Starting temperature. Flag important when random velocities are generated. • IG: Seed random number for velocity calculation • NTT: Temperature scaling • 0 Constant energy run. No scaling • 1 Constant T. Use Berendsen’s coupling • 4 When T deviates from TEMP0 more than DTEMP scale velocities, otherwise do not scale • TAUTP: Time constant for heat bath coupling: Default 1.0. Smaller value tighter coupling • VLIMIT: IF .ne.0 when velocity of one atom is >VLIMIT set velocity=VLIMIT

  20. Regulación de la presión(NTB=2) • NTP: Flag for constant pressure dynamics • 0 no constant pressure • 1 MD isotropic scaling • 2 MD anisotropic scaling • PRES0: Pressure (1 atm default). • COMP: Compressibility of the system. In general use water value (44.6) • TAUP: Pressure relaxation time (0.2 ps) • NPSCAL: Modelo de escalado posiciones • 0: atom scaling: can compress bonds. • 1: Molecule scaling

  21. SHAKE • NTC: Flag to use SHAKE (In general a good idea for normal systems) • 1 Do not use SHAKE • 2 SHAKE on X-H bonds • 3 SHAKE on all the bonds • TOL: Tolerance for coordinate resetting in SHAKE. Default 0.0005 Å.

  22. WATER CAP(gota de agua) • IVCAP: • 0 in effect if defined in parm • 1 Cap in effect, but pointer will be modified (MATCAP) • 2 Cap will be inactivated • FCAP: • Force constant for Cap (half harmonic). Default 1.5 kcal/mol Å2

  23. PARTICLE MESH EWALD • Es una técnica muy poderosa para incluir interacciones electrostática de largo alcance. • Es totalmente necesaria para simular DNA • Recomendable para proteínas, sobre todo si están muy cargadas • Sobreestima la periodicidad de la simulación. • Últimas versiones de AMBER lo toman como defecto de la simulación.

  24. PARTICLE MESH EWALD • &ewald namelist • A,B,C. The PME unit cell • Alpha,Beta,GAMMA: Cell angles • NFFT1,NFFT2,NFFT3: Size of charge grid. In general choose =A,B,C i.e grid spacing 1 Å • Use defaults for all the other parameters

  25. NMR REFINEMENT • La mayoría de usuarios usa MD solo para refinar la geometría a partir de las restricciones de distancias o ángulos derivadas a partir de otros programas DIANA, MARDIGRAS,... • Estas restricciones se introducen como “flat harmonic restraints” que se añaden al force-field. • Es posible introducir otras restricciones más elaboradas: Time averaged restrains, noesy volumes, dipolar couplings,...

  26. NMR REFINEMENT • ISCALE: Number of additional variables to optimize (in addition to 3N coordinates) • NOESKP: How often are the NOESY volumes computed • IPNLTY: • 1 minimize the abs value of errors (R-factor) • 2 minimize the RMS (sum square errors) • 3 Special treatment for NOESY intensities • MXSUB: Number of submolecules to be use def 1

  27. Restraints file • IRESID (restraints definition) • 0 global atom numbers • 1 global residue number • IAT(1)IAT(4) if IRESID=0 atoms to restraints (IAT(3)=0, distance, IAT(4)=0 angle, otherwise torsion). If IRESID=1 residue number, then ATNAM(1)ATNAM(2) define the atom #s. • NSTEP1, NSTEP2 use restraints only between these two integration steps. Def uses always 0 • IRSTYP: Absolute (0) or relative (1) restraints

  28. Restraints file • IALTD: Ignore large violation if 1. If 0 (default) not ignore • IFVARI: Change force or target value along the trajectory (R1AR4A, RK2ARK3A. • NINC, IMULT: Define how the target/force values change along the trajectory (use defaults).

  29. Restraints file • La forma del restraints es un pozo plano (si IALTD=0, default) • R1R4; RK2RK3; R1AR4A; RK2RK3 • Si R (valor en la simulación) • R<r1 o R>4. Liniar slope restraint • R2<R<R3 E=0 (flat) • Parabolic constraint otherwise • La forma del restraints varia para IALTD=1

  30. Restraints file • IGR1(i),i=1200. IGR2(i), =1200. Se usan para definir restraints sobre un grupo de átomos. Se calculan promedio de posiciones con esas listas

  31. Other restraints (used for NMR refinement) • Es posible incluir restraints adicionales • NOESY volume restraints • Chemical shifts restraints • Direct dipolar coupling restraints • Restraints de quiralidad • Time-averaged constraints • Se puede activar opción LES (multiple-copies)

More Related