Dear all, I am running md simulations on a decapeptide, using pressure coupling [npt]. My box is octahedral and box dimensions are set at peptide length plus twice the cut-off as recommended. I have set tau_p to be 1.0 ps. After 1 ns , the average pressure had come down to 2.6 bar, though fluctuations were quite high. [Standard deviation 150.8 ] But after 6ns, the pressure has risen again to 4.6 bar. Can you please advise me on this? Also, can you please tell me if there is any correlation between pressure average and tau_p values? I have attached the md parameters file and the mdout files with this mail. Thanks, Chetana.
title = MDP file for Full MD cpp = /lib/cpp integrator = MD tinit = 0 dt = 0.002 nstcomm = 1 nsteps = 500000 ; 1 ns (run control) nstxout = 10000 nstvout = 10000 nstxtcout = 250 nstenergy = 250 energygrps = Protein SOL ;(output control) nstlist = 10 ns_type = grid rlist = 1.1 ;(neighbor searching) coulombtype = PME ;rcoulomb_switch = 1.0 rcoulomb = 1.0 vdwtype = shift rvdw_switch = 0.9 rvdw = 1.0 fourierspacing = 0.12 ;(nm) ewald_rtol = 1e-5 pme_order = 4 ;(electrostatics and VDW) tcoupl = berendsen tc_grps = Protein SOL NA+ tau_t = 0.1 0.1 0.1 ref_t = 300 300 300;(Temperature coupling) ; pressure coupling is on pcoupl = berendsen tau_p = 1.0 compressibility = 4.5e-5 ref_p = 1.0 gen_vel = no constraints = all-bonds constraint_algorithm = lincs
; File 'mdout.mdp' was generated ; By user: chetana (501) ; On host: alanine ; At date: Mon Jan 1 12:28:06 2007 ;
; VARIOUS PREPROCESSING OPTIONS title = MDP file for Full MD cpp = /lib/cpp include = define = ; RUN CONTROL PARAMETERS integrator = MD ; Start time and timestep in ps tinit = 0 dt = 0.002 nsteps = 500000 ; For exact run continuation or redoing part of a run init_step = 0 ; mode for center of mass motion removal comm-mode = Linear ; number of steps for center of mass motion removal nstcomm = 1 ; group(s) for center of mass motion removal comm-grps = ; LANGEVIN DYNAMICS OPTIONS ; Temperature, friction coefficient (amu/ps) and random seed bd-temp = 300 bd-fric = 0 ld-seed = 1993 ; ENERGY MINIMIZATION OPTIONS ; Force tolerance and initial step-size emtol = 10 emstep = 0.01 ; Max number of iterations in relax_shells niter = 20 ; Step size (1/ps^2) for minimization of flexible constraints fcstep = 0 ; Frequency of steepest descents steps when doing CG nstcgsteep = 1000 nbfgscorr = 10 ; OUTPUT CONTROL OPTIONS ; Output frequency for coords (x), velocities (v) and forces (f) nstxout = 10000 nstvout = 10000 nstfout = 0 ; Checkpointing helps you continue after crashes nstcheckpoint = 1000 ; Output frequency for energies to log file and energy file nstlog = 100 nstenergy = 250 ; Output frequency and precision for xtc file nstxtcout = 250 xtc-precision = 1000 ; This selects the subset of atoms for the xtc file. You can ; select multiple groups. By default all atoms will be written. xtc-grps = ; Selection of energy groups energygrps = Protein SOL ; NEIGHBORSEARCHING PARAMETERS ; nblist update frequency nstlist = 10 ; ns algorithm (simple or grid) ns_type = grid ; Periodic boundary conditions: xyz (default), no (vacuum) ; or full (infinite systems only) pbc = xyz ; nblist cut-off rlist = 1.1 domain-decomposition = no ; OPTIONS FOR ELECTROSTATICS AND VDW ; Method for doing electrostatics coulombtype = PME rcoulomb-switch = 0 rcoulomb = 1.0 ; Dielectric constant (DC) for cut-off or DC of reaction field epsilon-r = 1 ; Method for doing Van der Waals vdwtype = shift ; cut-off lengths rvdw_switch = 0.9 rvdw = 1.0 ; Apply long range dispersion corrections for Energy and Pressure DispCorr = No ; Extension of the potential lookup tables beyond the cut-off table-extension = 1 ; Spacing for the PME/PPPM FFT grid fourierspacing = 0.12 ; FFT grid size, when a value is 0 fourierspacing will be used fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 ; EWALD/PME/PPPM parameters pme_order = 4 ewald_rtol = 1e-5 ewald_geometry = 3d epsilon_surface = 0 optimize_fft = no ; GENERALIZED BORN ELECTROSTATICS ; Algorithm for calculating Born radii gb_algorithm = Still ; Frequency of calculating the Born radii inside rlist nstgbradii = 1 ; Cutoff for Born radii calculation; the contribution from atoms ; between rlist and rgbradii is updated every nstlist steps rgbradii = 2 ; Salt concentration in M for Generalized Born models gb_saltconc = 0 ; IMPLICIT SOLVENT (for use with Generalized Born electrostatics) implicit_solvent = No ; OPTIONS FOR WEAK COUPLING ALGORITHMS ; Temperature coupling tcoupl = berendsen ; Groups to couple separately tc_grps = Protein SOL NA+ ; Time constant (ps) and reference temperature (K) tau_t = 0.1 0.1 0.1 ref_t = 300 300 300 ; Pressure coupling pcoupl = berendsen Pcoupltype = Isotropic ; Time constant (ps), compressibility (1/bar) and reference P (bar) tau_p = 1.0 compressibility = 4.5e-5 ref_p = 1.0 ; Random seed for Andersen thermostat andersen_seed = 815131 ; SIMULATED ANNEALING ; Type of annealing for each temperature group (no/single/periodic) annealing = ; Number of time points to use for specifying annealing in each group annealing_npoints = ; List of times at the annealing points for each group annealing_time = ; Temp. at each annealing point, for each group. annealing_temp = ; GENERATE VELOCITIES FOR STARTUP RUN gen_vel = no gen-temp = 300 gen-seed = 173529 ; OPTIONS FOR BONDS constraints = all-bonds ; Type of constraint algorithm constraint_algorithm = lincs ; Do not constrain the start configuration unconstrained-start = no ; Use successive overrelaxation to reduce the number of shake iterations Shake-SOR = no ; Relative tolerance of shake shake-tol = 1e-04 ; Highest order in the expansion of the constraint coupling matrix lincs-order = 4 ; Number of iterations in the final step of LINCS. 1 is fine for ; normal simulations, but use 2 to conserve energy in NVE runs. ; For energy minimization with constraints it should be 4 to 8. lincs-iter = 1 ; Lincs will write a warning to the stderr if in one step a bond ; rotates over more degrees than lincs-warnangle = 30 ; Convert harmonic bonds to morse potentials morse = no ; ENERGY GROUP EXCLUSIONS ; Pairs of energy groups for which all non-bonded interactions are excluded energygrp_excl = ; NMR refinement stuff ; Distance restraints type: No, Simple or Ensemble disre = No ; Force weighting of pairs in one distance restraint: Conservative or Equal disre-weighting = Conservative ; Use sqrt of the time averaged times the instantaneous violation disre-mixed = no
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