[gmx-users] Surface area calculation
Laura Leay
laura.leay at postgrad.manchester.ac.uk
Wed May 11 14:34:59 CEST 2011
Can anyone explain in detail the method that gromacs uses to calculate
surface area? Which surface area is it calculating (e.g., connolley,
accessible)?
I am under the impression that the final result is given in nm^2. Is
this correct?
Carrying out the surface area calculation in gromacs using the OPLS all
atom force field I obtain a value of 4.43 nm^2 for methane (carbon =
opls_138, sigma = 0.35 and hydrogen = opls_140, sigma = 0.25) (CT-HC
ideal bond length = 0.109, e=284512). The command was
g_sas -f conf.gro -s topol.tpr -oa -or -tv -probe 0.2 -ndots 200 -nopbc
and the result was taken from resarea.xvg
I have written a program to calculate the geometric accessible surface
area using the van der waals radius of the atoms and a probe of a given
size. The surface is defined from the centre of the probe. Using the
above values for sigma I obtain a value for methane of 1.15 nm^2 with a
probe diameter of 0.2 nm.
Obviously the two do not match and I am not sure why.
The individual atom areas for my molecule are:
C 0.22
H 0.24
H 0.23
H 0.22
H 0.24
Attached are the files used in the gromacs calculation along with the
output and my own program. If any one has any suggestions please let me
know.
-------------- next part --------------
# This file was created Wed May 11 13:05:56 2011
# by the following command:
# g_sas -f conf.gro -s topol.tpr -oa -or -tv -probe 0.2 -ndots 200 -nopbc
#
# g_sas is part of G R O M A C S:
#
# Gravel Rubs Often Many Awfully Cauterized Sores
#
@ title "Solvent Accessible Surface"
@ xaxis label "Time (ps)"
@ yaxis label "Area (nm\S2\N)"
@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 "Hydrophobic"
@ s1 legend "Hydrophilic"
@ s2 legend "Total"
@ s3 legend "D Gsolv"
0 4.43467 0 4.43467 -11.1328
-------------- next part --------------
# This file was created Wed May 11 13:05:56 2011
# by the following command:
# g_sas -f conf.gro -s topol.tpr -oa -or -tv -probe 0.2 -ndots 200 -nopbc
#
# g_sas is part of G R O M A C S:
#
# Gravel Rubs Often Many Awfully Cauterized Sores
#
@ title "Area per atom"
@ xaxis label "Atom #"
@ yaxis label "Area (nm\S2\N)"
@TYPE xy
1 1.53938 0.000291734
2 0.723823 0
3 0.723823 0
4 0.723823 0
5 0.723823 0
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methane
5
1DRG CT 1 0.000 0.000 0.000
1DRG HC 2 0.000 0.000 1.089
1DRG HC 3 1.027 0.000 -0.363
1DRG HC 4 -0.513 -0.889 -0.363
1DRG HC 5 -0.513 0.889 -0.363
7.90500 7.90500 7.90500
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; VARIOUS PREPROCESSING OPTIONS
title = Yo
cpp = /usr/bin/cpp
include =
define =
; RUN CONTROL PARAMETERS
integrator = steep
; Start time and timestep in ps
tinit = 0
dt = 0.002
nsteps = 1000
; 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 = 100
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 = 0
nstvout = 0
nstfout = 0
; Checkpointing helps you continue after crashes
nstcheckpoint = 1000
; Output frequency for energies to log file and energy file
nstlog = 50
nstenergy = 50
; Output frequency and precision for xtc file
nstxtcout = 50
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 =
; NEIGHBORSEARCHING PARAMETERS
; nblist update frequency
nstlist = 10
; 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 = 0.9
domain-decomposition = no
; OPTIONS FOR ELECTROSTATICS AND VDW
; Method for doing electrostatics
coulombtype = Cut-off
rcoulomb-switch = 0
rcoulomb = 0.9
; 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 = 0.9
; Apply long range dispersion corrections for Energy and Pressure
DispCorr = EnerPres
; 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 = no
; 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 = System
; Time constant (ps) and reference temperature (K)
tau_t = 0.1
ref_t = 300
; Pressure coupling
Pcoupl = berendsen
Pcoupltype = isotropic
; Time constant (ps), compressibility (1/bar) and reference P (bar)
tau_p = 1.0
compressibility = 4.5e-5
ref_p = 1.0
; Random seed for Andersen thermostat
andersen_seed = 815131
; SIMULATED ANNEALING
; Type of annealing for each temperature group (no/single/periodic)
annealing = no
; 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 = 300
gen_seed = 1993
; 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 =
-------------- next part --------------
[moleculetype]
; Name nrexcl
DRG 0
[ atoms ]
; nr type resnr resid atom cgnr charge mass
1 opls_138 1 DRG CT 1 0.000 12.0000
2 opls_140 1 DRG HC 1 0.000 01.0000
3 opls_140 1 DRG HC 1 0.000 01.0000
4 opls_140 1 DRG HC 1 0.000 01.0000
5 opls_140 1 DRG HC 1 0.000 01.0000
[ bonds ]
; i j func b0 kb
1 2 1 0.10800 284512.0
1 3 1 0.10800 284512.0
1 4 1 0.10800 284512.0
1 5 1 0.10800 284512.0
-------------- next part --------------
# This file was created Wed May 11 13:05:56 2011
# by the following command:
# g_sas -f conf.gro -s topol.tpr -oa -or -tv -probe 0.2 -ndots 200 -nopbc
#
# g_sas is part of G R O M A C S:
#
# Gravel Rubs Often Many Awfully Cauterized Sores
#
@ title "Area per residue"
@ xaxis label "Residue"
@ yaxis label "Area (nm\S2\N)"
@TYPE xy
1 4.43467 0
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