CHARMM c28a3 ace.doc

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                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

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
FOLDING CALCULATIONS, even though it has been successfully used for peptides
with less than 15 residues.

	 M. Schaefer & M. Karplus (1996) J. Phys. Chem. 100, 1578-1599.
         M. Schaefer, C. Bartels & M. Karplus (1998) J. Mol. Biol., in press.

* Menu:

* Syntax::      Syntax of the ACE specifications
* Defaults::    Defaults and Recommended values 
* Function::    Purpose of each of the specifications
* Examples::    Usage examples of the ACE module

File: ACE ]-[ Node: Syntax
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[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 ] [ IEPS real ] [ SEPS real ] [ ALPHa real ] [ SIGMa real ]

File: ACE ]-[ Node: Defaults
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The defaults for the ACE potential are
	IEPS	1.0
	SEPS	80.0
	ALPHa	1.2
	SIGMa	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
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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).

The ACE solvation potential has to be used together with no cutoff or with
atom based switching.

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 param19-1.2.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
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To set up simulations/minimizations with the ACE solvation potential,
the following energy call is expected to be adequate in most situations:

       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         Time      TOTEner        TOTKe       ENERgy  TEMPerature
DYNA PROP:             GRMS      HFCTote        HFCKe       EHFCor        VIRKe
DYNA INTERN:          BONDs       ANGLes       UREY-b    DIHEdrals    IMPRopers
DYNA EXTERN:        VDWaals         ELEC       HBONds          ASP         USER
DYNA PRESS:            VIRE         VIRI       PRESSE       PRESSI       VOLUme
DYNA ACE1:      HYDRophobic         SELF    SCREENing      COULomb 
DYNA ACE2:        SOLVation  INTERaction 
 ----------       ---------    ---------    ---------    ---------    ---------
DYNA>        0      0.00000  -3423.29671      0.00000  -3423.29671      0.00000
DYNA PROP>          4.45310  -3423.12228      0.52327      0.17442   -532.70519
DYNA INTERN>        6.58717     60.43092      0.00000     56.00750      7.32144
DYNA EXTERN>     -380.26218  -3173.38156      0.00000      0.00000      0.00000
DYNA PRESS>         0.00000    355.13679      0.00000      0.00000      0.00000
DYNA   ACE1>      109.04469  -3829.20991   2750.59427  -2203.81062
DYNA   ACE2>    -1078.61564    546.78365
 ----------       ---------    ---------    ---------    ---------    ---------
and the same during minimization (MINI...) or after
an energy calculation (ENER...).

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:   Interaction contribution to electrostatic solvation free energy,
             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

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.

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