CHARMM Element doc/ace.doc $Revision: 1.2 $
File: ACE, Node: Top, Up: (chmdoc/commands.doc), Next: Syntax
Analytical Continuum Solvent (ACS) Potential
Purpose: calculate solvation free energy and forces based on
a continuum description of the solvent, in particular the analytical
continuum electrostatics (ACE) potential.
Please report problems to Michael Schaefer at schaefer@brel.u-strasbg.fr
WARNING: The module is still being developed and may change in future
versions.
SERIOUS WARNING: The use of ACE in MD calculations may do harm to your
protein
and actually unfold it. DO NOT EXPECT THE POTENTIAL TO BE VIABLE FOR
PROTEIN
FOLDING CALCULATIONS, even though it has been successfully used for
peptides
with less than 15 residues.
REFERENCES:
M. Schaefer & M. Karplus (1996) J. Phys. Chem. 100, 1578-1599.
M. Schaefer, C. Bartels & M. Karplus (1998) J. Mol. Biol., in
press.
* Menu:
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Syntax::
Defaults::
Function::
Examples::
Syntax of the ACE specifications
Defaults and Recommended values
Purpose of each of the specifications
Usage examples of the ACE module
File: ACE, Node: Syntax, Up: Top, Previous: Top, Next: Defaults
Syntax
[SYNTAX ACE functions]
Syntax: The ACE specifications can be specified any time the nbond
specification parser is invoked, e.g.,
ENERgy [other-spec] [ace-spec]
ace-spec::=
[ ACE ] [ IEPS real ] [ SEPS real ] [ ALPHa real ] [ SIGMa real ]
File: ACE, Node: Defaults, Up: Top, Next: Function, Previous: Syntax
The defaults for the ACE potential are
IEPS
SEPS
ALPHa
SIGMa
1.0
80.0
1.2
3.0
In the current implementation, ACE should be used with united atom
parameters,
ALPHa set equal to 1.2 and the PARAM19 parameter file param19-1.2.inp;
the param19-1.2.inp file (in the ./test/data/ subdirectory) inludes a
table
of atom volumes at the end which is compatible with ALPHa 1.2.
File: ACE, Node: Function, Up: Top, Previous: Syntax, Next: Examples
0.
Introduction
The analytical continuum solvent (ACS) potential is introduced to
perform molecular dynamics/minimization calculations with a continuum
approximation of the solvent.
Two solvent contributions to the effective (free) energy of a solute
are included: the electrostatic solvation free energy, and the
non-polar (i.e., non-electrostatic) solvation free energy.
The first (electrostatic) contribution (G_el) is calculated using an
analytical approximation to the solution of the Poisson-equation
called ACE (from: analytical continuum electrostatics).
The non-polar solvation free energy (G_np) is approximated by a pairwise
potential which yields results that are very similar to the well-known
surface area approximations of the hydrophobic (solvation) energy
(e.g., Wesson and Eisenberg, Prot. Sci. 1 (1992), 227--235; see
the ASP potential in CHARMM).
Restriction:
The ACE solvation potential has to be used together with no cutoff or
with
atom based switching.
Compatibility:
1. ACE can be used with BLOCK (but: the diagonal elements of the BLOCK
matrix MUST NOT be zero).
2. ACE can be used with fixing atoms (CONS FIX); the resulting energy and
forces are an approximation, because all the interaction-dielectric terms
of the potential (eq (47) in Schaefer & Karplus, JPC 100 (1996), 1578)
which involve two fixed atoms are neglected, despite the fact that they
exist and that they are NOT invariant!
Meaning of the ACE parameters:
1. IEPS
Dielectric constant for the space occupied by the atoms that are
treated
explicitly, e.g., the space occupied by the protein.
2.
SEPS
Dielectric constant for the space occupied by the solvent that is
treated
as a continuum (i.e., the complement of the space occupied by the
protein).
3.
ALPHa
The volumes occupied by individual (protein) atoms are described by
Gaussian density distributions. The factor ALPHa controls the width of
these
Gaussians. The net volume of the individual atom Gaussian distributions
is
defined in the volume table at the end of the parameter file param191.2.inp.
The width of the atom volume distributions and the volume table have to
be consistent -- currently, the volumes in the param19-1.2.inp file are
optimal for an ALPHa of 1.2. Changing ALPHa without adapting the volume
table is expected to reduce the precision of the results.
4.
SIGMa
The ACE solvation potential includes a hydrophobic contribution
which is roughly proportional to the solvent accessible surface area.
The factor SIGMa scales the hydrophobic contribution. For peptides
with about 10-15 residues, a SIGMa factor of 3 results in hydrophobic
contributions that are approximately equal to the solvent accessible
surface area multiplied by 8 cal/(mol*A*A).
File: ACE, Node: Examples, Up: Top, Previous: Function, Next: Top
Examples
To set up simulations/minimizations with the ACE solvation potential,
the following energy call is expected to be adequate in most situations:
ENERgy ATOM ACE IEPS 1.0 SEPS 80.0 ALPHa 1.2 SIGMa 3 SWITch VDIS VSWI CUTNB 13.0 CTONNB 8.0 CTOFNB 12.0
When you run molecular dynamics or minimization with ACE, you get
two more lines in the log file printout with energy terms, e.g.,
DYNA DYN: Step
TEMPerature
DYNA PROP:
VIRKe
DYNA INTERN:
IMPRopers
DYNA EXTERN:
USER
Time
TOTEner
TOTKe
ENERgy
GRMS
HFCTote
HFCKe
EHFCor
BONDs
ANGLes
UREY-b
DIHEdrals
VDWaals
ELEC
HBONds
ASP
DYNA PRESS:
VIRE
VIRI
PRESSE
VOLUme
DYNA ACE1:
HYDRophobic
SELF
SCREENing
DYNA ACE2:
SOLVation INTERaction
--------------------------------------DYNA>
0
0.00000 -3423.29671
0.00000
0.00000
DYNA PROP>
4.45310 -3423.12228
0.52327
532.70519
DYNA INTERN>
6.58717
60.43092
0.00000
7.32144
DYNA EXTERN>
-380.26218 -3173.38156
0.00000
0.00000
DYNA PRESS>
0.00000
355.13679
0.00000
0.00000
DYNA
ACE1>
109.04469 -3829.20991
2750.59427
DYNA
ACE2>
-1078.61564
546.78365
--------------------------------------and the same during minimization (MINI...) or after
an energy calculation (ENER...).
PRESSI
COULomb
---------
---
-3423.29671
0.17442
-
56.00750
0.00000
0.00000
-2203.81062
---------
---
The terms in lines with ACE1 and ACE2 are:
HYDRophobic: Hydrophobic potential, equivalent to a surface based
solvation term proportional to the sigma input parameter;
SELF:
Self contribution to electrostatic solvation free energy,
Delta-E_self, first term of eq(8) (i.e., sum over all atomic
solvation energies, Delta-E_self_i, eq(28));
SCREENing:
energy,
Interaction contribution to electrostatic solvation free
i.e., screening of Coulomb interactions, eq(38) (sum over
all
atom pairs, including bonded and 1-3 atom pairs!);
COULomb:
Coulomb energy with constant dielectric of EPSI (sum over
all atom pairs for the first term in eq(36) -- excluding
bonded and 1-3 atom pairs, and 1-4 atom pair contributions
scaled with E14FAC);
SOLVation:
Electrostatic (!) solvation free energy, sum of SELF and
SCREENing;
INTERaction: Electrostatic interaction, sum of SCREENing and COULomb
(eq(36), but taking account of the bonded, 1-3, and 1-4
exclusion in the Coulomb term, see above).
The term "ELEC" in line "DYNA EXTERN>..." is the total electrostatic
energy:
ELEC:
Sum of SELF, SCREENing, COULomb.
Equation numbers refer to Schaefer & Karplus, J. Phys. Chem. 100 (1996),
1578.
see also: test cases c26test/ace1.inp and c26test/ace2.inp.