He, Yang wrote:
Hi all the users,
When I use the command "mdrun"to simulate the CG DNA model, I found that all
the files are output expect the trajectory file. I will list some parts of my mdp.file
During the simulation? Data is buffered, so you may not see immediate output.
Or is the trajectory absent at the end of the simulation? That might indicate a
problem with available disk space, depending on how large the file is.
-Justin
; RUN CONTROL PARAMETERS =
integrator = md
; start time and timestep in ps =
tinit = 0.0
dt = 0.03
nsteps = 1000000
; number of steps for center of mass motion removal =
nstcomm = 1
; OUTPUT CONTROL OPTIONS =
; Output frequency for coords (x), velocities (v) and forces (f) =
nstxout = 5000
nstvout = 5000
nstfout = 0
; Output frequency for energies to log file and energy file =
nstlog = 1000
nstenergy = 1000
; Output frequency and precision for xtc file =
nstxtcout = 1000
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 = plan1 NA CL W
; NEIGHBORSEARCHING PARAMETERS =
; nblist update frequency =
nstlist = 10
; ns algorithm (simple or grid) =
ns_type = grid
; Periodic boundary conditions: xyz or none =
pbc = xyz
; nblist cut-off =
rlist = 1.2
domain-decomposition = no
; OPTIONS FOR ELECTROSTATICS AND VDW =
; Method for doing electrostatics =
coulombtype = PME
rcoulomb_switch = 0.0
rcoulomb = 1.2
; Dielectric constant (DC) for cut-off or DC of reaction field =
epsilon_r = 20
; Method for doing Van der Waals =
vdw_type = Shift
; cut-off lengths =
rvdw_switch = 0.9
rvdw = 1.15
; Apply long range dispersion corrections for Energy and Pressure =
DispCorr = No
; Spacing for the PME/PPPM FFT grid =
fourierspacing = 0.3
; 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-05
epsilon_surface = 0
optimize_fft = yes
; OPTIONS FOR WEAK COUPLING ALGORITHMS =
; Temperature coupling =
tcoupl = Berendsen
; Groups to couple separately =
tc-grps = plan1 NA CL W
; Time constant (ps) and reference temperature (K) =
tau_t = 1.0 1.0 1.0 1.0
ref_t = 300 300 300 300
; Pressure coupling =
Pcoupl = no
Pcoupltype = Isotropic
; Time constant (ps), compressibility (1/bar) and reference P (bar) =
tau_p = 1.0
compressibility = 1e-5
ref_p = 1.0
; SIMULATED ANNEALING CONTROL =
annealing = no
; Time at which temperature should be zero (ps) =
zero_temp_time = 0
; GENERATE VELOCITIES FOR STARTUP RUN =
gen_vel = yes
gen_temp = 300
gen_seed = 473529
; OPTIONS FOR BONDS =
constraints = none
; Type of constraint algorithm =
constraint_algorithm = Lincs
; Do not constrain the start configuration =
unconstrained_start = no
; Relative tolerance of shake =
shake_tol = 0.0001
; Highest order in the expansion of the constraint coupling matrix =
lincs_order = 4
; 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
; NMR refinement stuff =
; Distance restraints type: No, Simple or Ensemble =
disre = No
; Force weighting of pairs in one distance restraint: Equal or Conservative =
disre_weighting = Equal
; Use sqrt of the time averaged times the instantaneous violation =
disre_mixed = no
disre_fc = 1000
disre_tau = 1.25
; Output frequency for pair distances to energy file =
nstdisreout = 100
; Free energy control stuff =
free_energy = no
init_lambda = 0
delta_lambda = 0
sc-alpha = 0
sc-sigma = 0.3
; Non-equilibrium MD stuff =
acc-grps =
accelerate =
freezegrps =
freezedim =
cos-acceleration =
energygrp_excl =
; Electric fields =
; Format is number of terms (int) and for all terms an amplitude (real) =
; and a phase angle (real) =
E-x =
E-xt =
E-y = 1 0.05 0.0
E-yt =
E-z =
E-zt =
; User defined thingies =
user1-grps =
user2-grps =
userint1 = 0
userint2 = 0
userint3 = 0
userint4 = 0
userreal1 = 0
userreal2 = 0
userreal3 = 0
userreal4 = 0
Any suggestions will be highly appreciated .
Thank you very much.
Yang
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--
========================================
Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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