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.
# 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
# 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
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
; 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 =
[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
# 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
#include "ffoplsaa.itp"
#include "methane.itp"
;#include "methnb.itp"
[System]
DRG
[Molecules]
DRG 1
program surface
!-------------------------------------------------------
!Adapted from code by Tina Duren (18/05/10 - program accessible_surface_area)
!to calculate the accessible surface area using Monte Carlo Integeration
!http://www.see.ed.ac.uk/~tduren/research/surface_area/ortho/program/accessible_surface_area.f90
!----------------------------------------------------
implicit none
integer, parameter:: maxatoms = 6000 !max number of atoms to be tested
integer, parameter:: nmonomers = 50 ! number of monomers in the chain
integer, parameter:: npoints = 200 !number of points to try per atom
real, parameter:: probe =2.0 !probe diameter in angstroms
!read in the xyz file
character(30) :: myfile(0:60)
integer:: natoms
integer::n
character(20):: title
character(2):: id(maxatoms)
real:: xatom(maxatoms), yatom(maxatoms), zatom(maxatoms)
!calculate the surface
real:: ratom(maxatoms) !the vdw sigma of the atom
Integer:: iseed !random number
Real:: ran0 !for generating random number from the function
real:: phi, costheta, theta !angles for generating random points
real, parameter:: pi = 3.14159
real:: xpoint, ypoint, zpoint !co-ords of a random point on the surface
real:: d !distance
integer:: naccept !counts the number of points accepted
real :: totalpoints !total number of points tried for the mol.
real:: atom_area, sum_area, mol_area !surface areas
integer:: i, j, k, ifile=0, pim !for do loops etc
integer :: flag !for counting overlaps
real:: wt(maxatoms) !atomic mass
real:: mass !mass of the chain
!------------------------------------------------------------------------
! Seed for random number generator, change if you want to start from a
! different random number.
iseed=-5213150
! to properly initialise the random number generator, a negative seed
! is needeed
If (iseed > 0) iseed = -1 * iseed
!--------------------------------------------------------
!read in the xyz file
myfile(0)='PIM-PI-1/pim_1000.xyz'
myfile(1)='PIM-PI-1/pim_1001.xyz'
myfile(2)='PIM-PI-1/pim_1002.xyz'
myfile(3)='PIM-PI-1/pim_1003.xyz'
myfile(4)='PIM-PI-1/pim_1004.xyz'
myfile(5)='PIM-PI-1/pim_1005.xyz'
myfile(6)='PIM-PI-1/pim_1006.xyz'
myfile(7)='PIM-PI-1/pim_1007.xyz'
myfile(8)='PIM-PI-1/pim_1008.xyz'
myfile(9)='PIM-PI-1/pim_1009.xyz'
myfile(10)='PIM-PI-2/pim_1001.xyz'
myfile(11)='PIM-PI-2/pim_1002.xyz'
myfile(12)='PIM-PI-2/pim_1003.xyz'
myfile(13)='PIM-PI-2/pim_1004.xyz'
myfile(14)='PIM-PI-2/pim_1005.xyz'
myfile(15)='PIM-PI-2/pim_1006.xyz'
myfile(16)='PIM-PI-2/pim_1007.xyz'
myfile(17)='PIM-PI-2/pim_1008.xyz'
myfile(18)='PIM-PI-2/pim_1009.xyz'
myfile(19)='PIM-PI-2/pim_1010.xyz'
myfile(20)='PIM-PI-3/pim_1001.xyz'
myfile(21)='PIM-PI-3/pim_1002.xyz'
myfile(22)='PIM-PI-3/pim_1003.xyz'
myfile(23)='PIM-PI-3/pim_1004.xyz'
myfile(24)='PIM-PI-3/pim_1005.xyz'
myfile(25)='PIM-PI-3/pim_1006.xyz'
myfile(26)='PIM-PI-3/pim_1007.xyz'
myfile(27)='PIM-PI-3/pim_1008.xyz'
myfile(28)='PIM-PI-3/pim_1009.xyz'
myfile(29)='PIM-PI-3/pim_1010.xyz'
myfile(30)='PIM-PI-4/pim_1001.xyz'
myfile(31)='PIM-PI-4/pim_1002.xyz'
myfile(32)='PIM-PI-4/pim_1003.xyz'
myfile(33)='PIM-PI-4/pim_1004.xyz'
myfile(34)='PIM-PI-4/pim_1005.xyz'
myfile(35)='PIM-PI-4/pim_1006.xyz'
myfile(36)='PIM-PI-4/pim_1007.xyz'
myfile(37)='PIM-PI-4/pim_1008.xyz'
myfile(38)='PIM-PI-4/pim_1009.xyz'
myfile(39)='PIM-PI-4/pim_1010.xyz'
myfile(40)='PIM-PI-7/pim_1000.xyz'
myfile(41)='PIM-PI-7/pim_1001.xyz'
myfile(42)='PIM-PI-7/pim_1002.xyz'
myfile(43)='PIM-PI-7/pim_1003.xyz'
myfile(44)='PIM-PI-7/pim_1004.xyz'
myfile(45)='PIM-PI-7/pim_1005.xyz'
myfile(46)='PIM-PI-7/pim_1006.xyz'
myfile(47)='PIM-PI-7/pim_1007.xyz'
myfile(48)='PIM-PI-7/pim_1008.xyz'
myfile(49)='PIM-PI-7/pim_1009.xyz'
myfile(50)='PIM-PI-8/pim_1000.xyz'
myfile(51)='PIM-PI-8/pim_1001.xyz'
myfile(52)='PIM-PI-8/pim_1002.xyz'
myfile(53)='PIM-PI-8/pim_1003.xyz'
myfile(54)='PIM-PI-8/pim_1004.xyz'
myfile(55)='PIM-PI-8/pim_1005.xyz'
myfile(56)='PIM-PI-8/pim_1006.xyz'
myfile(57)='PIM-PI-8/pim_1007.xyz'
myfile(58)='PIM-PI-8/pim_1008.xyz'
myfile(59)='PIM-PI-8/pim_1009.xyz'
open(40,file='output.txt')
write(40,*) 'nmonomers:', nmonomers, ' npoints:', npoints, ' probe diameter:', probe
do pim=0,1
!pim = 5
! if (pim==0) then
! write (40,*)'PIM-PI-1'
! natoms =93*nmonomers
! else if (pim==1) then
! write (40,*)'PIM-PI-2'
! natoms =106*nmonomers
! else if (pim==2) then
! write (40,*)'PIM-PI-3'
! natoms =100*nmonomers
! else if (pim==3) then
! write (40,*)'PIM-PI-4'
! natoms =97*nmonomers
! else if (pim==4) then
! write (40,*)'PIM-PI-7'
! natoms =87*nmonomers
! else ! (pim==5) then
! write (40,*)'PIM-PI-8'
! natoms =109*nmonomers
! end if
if (pim==0) then
write(40,*)'Argon'
natoms = 1
open(10,file='Argon.xyz')
print*,'opened argon'
else if(pim==1)then
write(40,*)'Methane'
natoms = 5
open(10,file='methane.xyz')
print*,'opened methane'
end if
!do ifile=0,9
!ifile = 0
! open(10,file=myfile(pim*10+ifile))
read(10,*) n !1st line in the file is the no. of atoms
!if(n > maxatoms) then
! Print*, 'Too many atoms found in xyz file'
! stop
!end if
read (10,*) title !2nd line of the file is the molecule name
print*,title
if(pim==0)then
read(10,*) id(1), xatom(1), yatom(1), zatom(1)
else
do i=1,natoms !reads in the co-ordinates
read(10,*) id(i), xatom(i), yatom(i), zatom(i)
!print*, i, id(i), xatom(i), yatom(i), zatom(i)
end do
end if
close (10)
!----------------calculate the surface-----------------------------------
!assign Van der Waals radii to the atoms
mass = 0.0
do i=1,natoms
if (id(i)== 'C') then
ratom(i)= 3.5
wt(i)=12.0
else if(id(i) == 'Ar') then
ratom(i)= 3.5 !OPLS_135 (CT)
wt(i) = 40.0
else !id == H
ratom(i) = 2.5
wt(i) = 1.0
end if
print*, id(i), ratom(i)
mass = mass + wt(i)
end do
print*,mass
!place a random point on an atom's surface and
!find the distance to all other atoms
!count the no. of points that do not lie wthin the radius of another atom
sum_area = 0.0
do i=1,natoms !loop over all atoms in chain
naccept = 0
do j=1,npoints !generate random points on surface of atom
! print*, 'calculating point ', j, ' of atom ', i, NACCEPT
! Generate random vector of length 1
! First generate phi 0:+2pi
phi = ran0(iseed)*2.0*pi
! Generate cosTheta -1:1 to allow for even distribution of random vectors
! on the unit sphere.See http://mathworld.wolfram.com/SpherePointPicking.html
! for further explanations
costheta = 1 - ran0(iseed) * 2.0
theta = Acos(costheta)
xpoint = sin(theta)*cos(phi)
ypoint = sin(theta)*sin(phi)
zpoint = costheta
! Make this vector of length (sigma+probe_diameter)/2.0
xpoint = xpoint*(ratom(i)+probe)/2.0
ypoint = ypoint*(ratom(i)+probe)/2.0
zpoint = zpoint*(ratom(i)+probe)/2.0
! Translate the center of coordinate to the particle i center and apply PBC
xpoint = xpoint + xatom(i)
ypoint = ypoint + yatom(i)
zpoint = zpoint + zatom(i)
flag=0
do k=1, natoms !find distance to surface of all other atoms
if(flag==0) then
if(k == i) cycle
d = sqrt((xpoint-xatom(k))**2+(ypoint-yatom(k))**2+(zpoint-zatom(k))**2)
if ( d < (ratom(k)+probe)/2. ) flag=1
endif
end do
if(flag==0) naccept=naccept+1
end do !j loop -npoints
!PRINT*, 'FINISH LOOP'
!use the fraction of points accepted to find the surface area of the chain
totalpoints = REAL(naccept)/REAL(npoints) !fraction of points accepted for atom i
! PRINT*, 'TOTALPOINTS',TOTALPOINTS,NACCEPT,NPOINTS
! print*, 'i',i, ratom(i)
atom_area = 4.0*pi*((ratom(i)+probe)/2.)**2 * totalpoints !surface area of atom
print*,naccept, atom_area
sum_area = sum_area + atom_area !surface area of all the atoms
end do !i loop -natoms
write(40,*) ifile+1,':: ', sum_area, ' Asq. ', sum_area*(6.023e23/1.e20)/mass , ' msq/gram'
print*, '---------- Chain', ifile+1, 'of PIM-PI-',pim+1,'----------'
print*, 'The surface area of the chain is:', sum_area, ' Angstroms squared'
print*, 'This is:', sum_area*(6.023e23/1.e20)/mass , ' metres squared per gram'
!end do !myfile
end do !pim
close(40)
end program surface
!----------------FUNCTIONS-------------------------------------
FUNCTION ran0(idum)
!
! Random number generator from W.H. Press et al, Numerical Recipes in
! FORTRAN, Cambridge University Press, 1992
!
INTEGER idum,IA,IM,IQ,IR,NTAB,NDIV
REAL ran0,AM,EPS,RNMX
PARAMETER (IA=16807,IM=2147483647,AM=1./IM,IQ=127773,IR=2836, &
NTAB=32,NDIV=1+(IM-1)/NTAB,EPS=1.2e-7,RNMX=1.-EPS)
INTEGER j,k,iv(NTAB),iy
SAVE iv,iy
DATA iv /NTAB*0/, iy /0/
if (idum.le.0.or.iy.eq.0) then
idum=max(-idum,1)
do 11 j=NTAB+8,1,-1
k=idum/IQ
idum=IA*(idum-k*IQ)-IR*k
if (idum.lt.0) idum=idum+IM
if (j.le.NTAB) iv(j)=idum
11 continue
iy=iv(1)
endif
k=idum/IQ
idum=IA*(idum-k*IQ)-IR*k
if (idum.lt.0) idum=idum+IM
j=1+iy/NDIV
iy=iv(j)
iv(j)=idum
ran0=min(AM*iy,RNMX)
return
END FUNCTION ran0
--
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