Hi:
I am working on membrane simulation under lipid (DPPC, from Peter
Tieleman group site). I equilibrated dppc membrane for 10 ns and when
i got the area by lipid (x*y/ # lipids) using g_energy, i obtained
that the area is constant (0.64), there isn't any fluctuaction during
10 ns..althougth the volumen isn't constant.
What's wrong in this simulation?
Any help will be highly appreciated. Thanks
Maite
These g_energy output:
----------------------------------------------------------
@ legend length 2
@ s0 legend "Kinetic-En."
@ s1 legend "Total-Energy"
@ s2 legend "Temperature"
@ s3 legend "Pressure-(bar)"
@ s4 legend "Box-X"
@ s5 legend "Box-Y"
@ s6 legend "Box-Z"
@ s7 legend "Volume"
@ s8 legend "Density-(SI)"
@ s9 legend "T-DPP"
@ s10 legend "T-SOL"
0.000000 44884.128906 -299551.125000 309.756866 -2867.529297
6.369600 6.399800 6.680000 272.304596 974.509155 312.786591
307.970825
20.000000 44859.781250 -252572.656250 309.588837 62.661823
6.369600 6.399800 6.516144 265.625153 999.014282 310.579834
309.004639
40.000000 44840.101562 -252600.875000 309.453064 -93.168358
6.369600 6.399800 6.494525 264.743896 1002.339722 306.650665
311.105103
60.000004 45093.398438 -253077.312500 311.201111 -99.019768
6.369600 6.399800 6.491228 264.609497 1002.848877 310.111328
311.843567
80.000000 45020.613281 -252663.734375 310.698822 19.632711
6.369600 6.399800 6.504295 265.142151 1000.834167 309.710663
311.281342
100.000008 44901.433594 -252496.687500 309.876312 122.716400
6.369600 6.399800 6.506715 265.240784 1000.461975 312.459656
308.353394
120.000008 44964.890625 -252896.796875 310.314270 -124.685959
6.369600 6.399800 6.514557 265.560486 999.257568 306.510254
312.556793
140.000000 45168.968750 -252813.281250 311.722626 -290.249481
6.369600 6.399800 6.488441 264.495850 1003.279724 312.059570
311.524017
160.000000 44465.328125 -253265.328125 306.866638 368.317017
6.369600 6.399800 6.500315 264.979919 1001.446960 307.570343
306.451813
180.000015 44680.867188 -252064.906250 308.354126 -243.635345
6.369600 6.399800 6.491784 264.632141 1002.763062 309.213043
307.847809
200.000015 44827.578125 -252667.828125 309.366638 -166.550201
6.369600 6.399800 6.477999 264.070221 1004.896851 308.571106
309.835602
220.000015 44968.542969 -253124.671875 310.339447 -171.839508
6.369600 6.399800 6.487612 264.462097 1003.407837 309.458679
310.858673
240.000015 44708.015625 -253120.671875 308.541504 203.768204
6.369600 6.399800 6.498459 264.904236 1001.733032 307.988251
308.867645
2..............
---------------------------------------------------------------------------------------------
These is my .mdp file
---------------------------------------------------------------------------------------------
; VARIOUS PREPROCESSING OPTIONS
title = DM com Restricoes
cpp = /lib/cpp
include =
define =
; RUN CONTROL PARAMETERS
integrator = md
; Start time and timestep in ps
tinit = 0
dt = 0.002
nsteps = 1500000 ; = 3000.0 ps
; 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 = 1000
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 = 50000
nstvout = 50000
nstfout = 50000
; Checkpointing helps you continue after crashes
nstcheckpoint = 1000
; Output frequency for energies to log file and energy file
nstlog = 1000
nstenergy = 10
; Output frequency and precision for xtc file
nstxtcout = 500
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 = DPP SOL
; NEIGHBORSEARCHING PARAMETERS
; nblist update frequency
nstlist = 5
; 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
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
vdw-type = Cut-off
; cut-off lengths
rvdw-switch = 0
rvdw = 1.4
; 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-05
ewald_geometry = 3d
epsilon_surface = 0
optimize_fft = yes
; 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 = DPP SOL
; Time constant (ps) and reference temperature (K)
tau-t = 0.1 0.1
ref-t = 310 310
; Pressure coupling
Pcoupl = berendsen
Pcoupltype = semiisotropic
; Time constant (ps), compressibility (1/bar) and reference P (bar)
tau-p = 0.5 0.5
compressibility = 0 4.5e-5
ref-p = 0 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 = yes
gen-temp = 310.0
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
disre-fc = 1000
disre-tau = 0
; Output frequency for pair distances to energy file
nstdisreout = 100
; Orientation restraints: No or Yes
orire = no
; Orientation restraints force constant and tau for time averaging
orire-fc = 0
orire-tau = 0
orire-fitgrp =
; Output frequency for trace(SD) to energy file
nstorireout = 100
; Dihedral angle restraints: No, Simple or Ensemble
dihre = No
dihre-fc = 1000
dihre-tau = 0
; Output frequency for dihedral values to energy file
nstdihreout = 100
; Free energy control stuff
free-energy = no
init-lambda = 0
delta-lambda = 0
sc-alpha = 0
sc-sigma = 0.3
-----------------------------------------------------------------------------------------------------
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