[gmx-users] area by lipid
Alan Dodd
anoddlad at yahoo.com
Sun Nov 25 01:23:16 CET 2007
Yes. Compressibility of 0 for X/Y dimensions would tend to result in a static (i.e., non-compressible!) box.
Look for some papers on lipid simulations - excessively low area/headgroup is a common problem, and there are a variety of opinions on how to approach this.
----- Original Message ----
From: maite lopez cabezas <lopezmai at gmail.com>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Sent: Sunday, November 25, 2007 12:02:22 AM
Subject: Re: [gmx-users] area by lipid
Thanks Alan
I tried with traj too and it's the same result....somebody use
g_energy or g_traj. The cuestion is having x and y. The problem is I
want to simulated a peptide-membrane system and the area couldn't be
constant cause the insertion of the peptide increases the bilayer
area. I think that is the compressibility , i changed my parameters
from
compressibility = 0 4.5e-5
ref-p = 0 1.0
to
compressibility =4.5e-5 4.5e-5
ref-p = 1.0 1.0
and the area changed from 0.645 to 0.62 and it isn't a good valor.
Maite
These the output traj -ob
# g_traj_331 -ob box.xvg -f dppc128_3ns_ok.xtc -e 1000 -s 3.tpr -nice 0
#
# g_traj_331 is part of G R O M A C S:
#
# Grunge ROck MAChoS
#
@ title "Box vector elements"
@ xaxis label "Time (ps)"
@ yaxis label "(nm)"
@TYPE xy
@ view 0.15, 0.15, 0.75, 0.85
@ legend on
@ legend box on
@ legend loctype view
@ legend 0.78, 0.8
@ legend length 2
@ s0 legend "XX"
@ s1 legend "YY"
@ s2 legend "ZZ"
@ s3 legend "YX"
@ s4 legend "ZX"
@ s5 legend "ZY"
0 6.3696 6.3998 6.68 0 0 0
1 6.3696 6.3998 6.64996 0 0 0
2 6.3696 6.3998 6.63114 0 0 0
3 6.3696 6.3998 6.60618 0 0 0
4 6.3696 6.3998 6.59534 0 0 0
5 6.3696 6.3998 6.5969 0 0 0
6 6.3696 6.3998 6.58594 0 0 0
7 6.3696 6.3998 6.57235 0 0 0
8 6.3696 6.3998 6.57301 0 0 0
9 6.3696 6.3998 6.55283 0 0 0
10 6.3696 6.3998 6.5441 0 0 0
11 6.3696 6.3998 6.52643 0 0 0
12 6.3696 6.3998 6.54106 0 0 0
13 6.3696 6.3998 6.53806 0 0 0
14 6.3696 6.3998 6.54126 0 0 0
15 6.3696 6.3998 6.53768 0 0 0
On Nov 24, 2007 6:00 PM, Alan Dodd <anoddlad at yahoo.com> wrote:
> I didn't think g_energy was useful for that - I've always used g_traj -ob to get box dimensions. If noone has a better answer, you should probably just try that and see if you get the same effect.
>
>
> ----- Original Message ----
> From: maite lopez cabezas <lopezmai at gmail.com>
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Sent: Saturday, November 24, 2007 10:01:24 PM
> Subject: [gmx-users] area by lipid
>
>
> 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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