[gmx-users] area by lipid

Alan Dodd anoddlad at yahoo.com
Sun Nov 25 00:00:16 CET 2007


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
-----------------------------------------------------------------------------------------------------
_______________________________________________
gmx-users mailing list    gmx-users at gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before
 posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-request at gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php





      ____________________________________________________________________________________
Be a better sports nut!  Let your teams follow you 
with Yahoo Mobile. Try it now.  http://mobile.yahoo.com/sports;_ylt=At9_qDKvtAbMuh1G1SQtBI7ntAcJ



More information about the gromacs.org_gmx-users mailing list