[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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