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FACTS: Fast Analytical Continuum Treatment of Solvation

Note

Questions and comments regarding FACTS should be directed to

Amedeo Caflisch (caflisch@bioc.uzh.ch)

Reference for FACTS:

  1. Haberthuer and Caflisch, J. Comput. Chem., 29(5): 701-715, 2008 DOI: 10.1002/jcc.20832

Description

FACTS is an efficient generalized Born implicit solvent model [1].Because of its speed it is particularly useful for MD simulations. It is based on the fully analytical evaluation of the volume and spatial symmetry of the solvent that is displaced from around a solute atom by its neighboring atoms. The two measures of solvent displacement are combined in empirical equations to approximate the atomic (or self) electrostatic solvation energy and the solvent accessible surface area. The former directly yields the effective Born radius, which is used in the generalized Born formula to calculate the solvent-screened electrostatic interaction energy. The solvent accessible surface area is used to approximate the non-polar contribution to solvation. FACTS is only four times slower than using the vacuum energy in molecular dynamics simulations of peptides and proteins.

FACTS can be used with either force field “param19” or “param22/27”, but parameters were derived for protein atoms only. Parameters for unknown atom types can be extrapolated from known ones with the “TAVW” option (see below).

Periodic boundary condition can be set up with the CHARMM IMAGE facility and the FACTS “TAIM” option.

The FACTS algorithm has been parallelized in 2007 by F.Marchand (fmarchand@bioc.uzh.ch).

Syntax of the FACTS Command

FACTs {TCPS 19} {TEPS 1.0} [TKPS real] [GAMM real]
      {TCPS 22} {TEPS 2.0} [TAIM] [TAVW] [TPSL]

Description of the FACTS keywords and options

Keyword Default Purpose
TCPS 19 Force-field specific, either 19 or 22. TCPS 22 also works with param27, although only protein atoms are parametrized.
TEPS 1.0 Solute dielectric constant. One can specify only TEPS = 1.0 or TEPS = 2.0, since only these values were used as interior dielectric constant for the finite-difference Poisson calculation of atomic solvation energies used to parametrize FACTS.
TKPS 4.0 Kappa, the factor in the denominator of the exponential function in the Generalized Born formula. It usually ranges between 4.0 (Still’s original equation) and 8.0.
GAMM 0.015 Nonpolar surface tension coefficients in kcal/(molxA^2).
TAIM false Flag to include contribution from image atoms. The FACTS module works with the CHARMM IMAGE facility. This flag should be included in the FACTS command line if images (PBC) are used.
TAVW false FACTS distinguishes atoms solely based on their VdW radius and only atoms found in proteins are currently parametrized. If a system contains atoms whose radii are not among those already parametrized in FACTS, then the “TAVW” option will extrapolate new parameters from already parametrized atoms.
TPSL false Flag to print detailed information about the atomic self-electrostatic contribution to the energy.

Examples

PARAM 19

REMARK: It was observed that (for param19) FACTS performs better with
the dielectric constant set to 2.0 rather than to 1.0.
! ------------------------------------------------------------------
!
!  large, globular systems (e.g., protein in folded state)
!  epsilon=2.0 and gamma=0.025

set diele 2.0

nbond nbxmod 5 atom cdiel eps @diele shift vatom vdistance vshift -
      cutnb 9.0 ctofnb 7.5 ctonnb 6.5 e14fac 0.4 wmin 1.5

scalar wmain = radius
scalar wmain set 1.0 selection (type h*) end

facts tcps 19 teps @diele gamm 0.025

! ------------------------------------------------------------------
!
!  Reversible folding simulations of structured peptides
!  epsilon=2.0 and gamma=0.015

set diele 2.0

nbond nbxmod 5 atom cdiel eps @diele shift vatom vdistance vshift -
      cutnb 9.0 ctofnb 7.5 ctonnb 6.5 e14fac 0.4 wmin 1.5

scalar wmain = radius
scalar wmain set 1.0 selection (type h*) end

facts tcps 19 teps @diele gamm 0.015

! ------------------------------------------------------------------
!
!  Unstructured peptides and peptide aggregation
!  epsilon=2.0 and gamma=0.0075

set diele 2.0

nbond nbxmod 5 atom cdiel eps @diele shift vatom vdistance vshift -
      cutnb 9.0 ctofnb 7.5 ctonnb 6.5 e14fac 0.4 wmin 1.5

scalar wmain = radius
scalar wmain set 1.0 selection (type h*) end

facts tcps 19 teps @diele gamm 0.0075

! ------------------------------------------------------------------
!
!  Periodic Boundary Conditions
!  (images should be previously set up with the IMAGE facility)
!  Print detailed informations about the atomic self-electrostatic
!  contributions to the energy
!  epsilon=1.0 and gamma=0.015

set diele 2.0

nbond nbxmod 5 atom cdiel eps @diele shift vatom vdistance vshift -
      cutnb 9.0 ctofnb 7.5 ctonnb 6.5 e14fac 0.4 wmin 1.5

scalar wmain = radius
scalar wmain set 1.0 selection (type h*) end

facts tcps 19 teps @diele gamm 0.015 taim tpsl

PARAM 22

!  epsilon=1.0 and gamma=0.015

set diele 1.0

nbond nbxmod 5 atom cdiel eps @diele shift vatom vdistance vswitch -
      cutnb 14.0 ctofnb 12.0 ctonnb 10.0 e14fac 1.0 wmin 1.5

scalar wmain = radius

facts tcps 22 teps @diele gamm 0.015

See also: test cases

  • ~/charmm/test/c35test/facts_p19.inp
  • ~/charmm/test/c35test/facts_p22.inp