File: apolar.xml

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<cmdsynopsis>
	<command>APOLAR</command>
	<arg choice="opt" id="elec-name">name <replaceable>id</replaceable></arg>
	<arg choice="opt" rep="repeat"><replaceable>keywords</replaceable></arg>
	<command>END</command>
</cmdsynopsis>
<para>This section is the main component for apolar solvation calculations in
	APBS runs. There may be several <command>APOLAR</command> sections,
	operating on different molecules or using different parameters for
	multiple runs on the same molecule. The order of the
	<command>APOLAR</command> statement matters (see above); the arguments
	are:
	<variablelist>
		<varlistentry>
			<term> name <replaceable>id</replaceable> </term>
			<listitem>
				<para>This optional command allows users to
					assign an alphanumeric string to the
					calculation to facilitate later
					operations (particularly in the 
					<link linkend="print"><command>PRINT</command></link> statements).
				</para>
			</listitem>
		</varlistentry>
		<varlistentry>
			<term> <replaceable>keywords</replaceable> </term>
			<listitem>
				<para>Keywords describing the parameters of the
					apolar calculation.  These are
					described in
					<xref linkend="apolar-keywords-sect"/>.
				</para>
			</listitem>
		</varlistentry>
	</variablelist>
</para>

<sect3 id="apolar-basic"> <title>Basic apolar solvation calculations</title>

	<para>
		APBS apolar calculations follow the very generic framework
		described in:
	</para>
	<para>
		Wagoner JA, Baker NA. Assessing implicit models for nonpolar
		mean solvation forces: the importance of dispersion and volume
		terms. Proc Natl Acad Sci USA, 103, 8331-8336, 2006.
		(<ulink url="http://dx.doi.org/10.1073/pnas.0600118103">http://dx.doi.org/10.1073/pnas.0600118103</ulink>)
	</para>
	<para>In particular, nonpolar solvation potentials of mean force
		(energies) are calculated according to <xref
			linkend="eqn-nonpolar-energy"/>.
		<equation id="eqn-nonpolar-energy"> <title>Nonpolar solvation potentials of mean
				force</title>
			<alt>gamma A + p V + integral</alt>
			<graphic fileref="images/nonpolar-energy.png"/>
		</equation>
		Mean nonpolar solvation forces are calculated according to
		<xref linkend="eqn-nonpolar-force"/>.
		<equation id="eqn-nonpolar-force"> <title>Nonpolar solvation
				mean forces</title>
			<alt>gamma dA + p dV + dintegral</alt>
			<graphic fileref="images/nonpolar-force.png"/>
		</equation>
		In these equations, 
		gamma (see <link linkend="apolar-gamma">gamma</link> below) 
		is the repulsive (hard sphere) solvent surface tension, 
		A is the conformation-dependent solute surface area
		(see <link linkend="apolar-srad">srad</link> 
		and <link linkend="apolar-srfm">srfm</link> below),
		p (see <link linkend="apolar-press">press</link> below) 
		is the repulsive (hard sphere) solvent pressure, 
		V is the conformation-dependent solute volume
		(see <link linkend="apolar-srad">srad</link> 
		and <link linkend="apolar-srfm">srfm</link> below),
		rho (see <link linkend="apolar-bconc">bconc</link> below) 
		is the bulk solvent density, 
		and the integral involves the
		attractive portion (defined in a Weeks-Chandler-Andersen sense)
		of the Lennard-Jones interactions between the solute and the
		solvent integrated over the region of the problem domain
		<emphasis>outside</emphasis> the solute volume V
		(see <link linkend="apolar-srad">srad</link> 
		and <link linkend="apolar-srfm">srfm</link> below).
		Lennard-Jones parameters are taken from APBS parameter files
		(see <xref linkend="parm-xml-format"/>) as read in through an
		APBS input file <link linkend="read">READ</link> statement.
	</para>

	<important>
		<para>All apolar calculations require a <link
				linkend="param-format">parameter file</link>
			which contains Lennard-Jones radius and well-depth
			parameters for all the atoms in the solute PDB.  This
			parameter file must also contain radius and well-depth
			parameters for water (specifically:  residue "WAT" and
			atom "OW").</para>
	</important>

	<para>
		Note that the above expressions can easily be reduced to
		simpler apolar solvation formalisms by setting one or more of
		the coefficients (gamma, rho, and p) to zero through the
		keywords below.
	</para>

</sect3>

<sect3 id="apolar-keywords-sect"> <title>Keyword descriptions</title>
	<para>
		This is a list of keywords used in the <command>APOLAR</command> statements of APBS.  
	</para>
	<itemizedlist>

		<listitem id="apolar-bconc">
			<cmdsynopsis>
				<command>bconc</command>
				<arg choice="req"><replaceable>bulk solvent
						density</replaceable></arg>
			</cmdsynopsis>
			<para>Specify the bulk solvent density in
				&Aring;<superscript>-3</superscript>. This
				coefficient multiplies the integral term of the
				apolar model discussed above and can be set to
				zero to eliminate integral contributions to the
				apolar solvation calculation.</para>
			<variablelist>
				<varlistentry>
					<term><replaceable>bulk solvent
							density</replaceable></term>
					<listitem><para>Bulk solvent density
							(in
							&Aring;<superscript>-3</superscript>)</para></listitem>
				</varlistentry>
			</variablelist>
		</listitem>


		<listitem id="apolar-calcenergy">
			<cmdsynopsis>
				<command>calcenergy</command>
				<arg choice="req"> <replaceable>flag</replaceable> </arg>
			</cmdsynopsis>
			<para>
				This optional keyword controls electrostatic
				energy output from an apolar solvation calculation.
				<note>
					<para> Note that this option must be used consistently for all
						calculations that will appear in subsequent 
						<link linkend="print"><command>PRINT</command></link> statements.
						For example, if the statement <literal>print energy 1 - 2
							end</literal> appears in the input file, then both calculations 1
						and 2 must have <command>calcenergy</command> keywords present with
						the same values for <replaceable>flag</replaceable>.
					</para>
				</note>
				<variablelist>
					<varlistentry>
						<term> <replaceable>flag</replaceable> </term>
						<listitem>
							<para>Specify the types of energy values to be returned:
								<variablelist>
									<varlistentry>
										<term>no</term>
										<listitem>
											<para>(Deprecated) don't calculate any energies.</para>
										</listitem>
									</varlistentry>
									<varlistentry>
										<term>total</term>
										<listitem>
											<para>Calculate
												and
												return
												total
												apolar energy for
												the entire molecule.</para>
										</listitem>
									</varlistentry>
									<varlistentry>
										<term>comps</term>
										<listitem>
											<para>Calculate
												and
												return
												total
												apolar energy for
												the entire molecule as well as electrostatic energy
												components for each atom.</para>
										</listitem>
									</varlistentry>
								</variablelist>
							</para>
						</listitem>
					</varlistentry>
				</variablelist>
			</para>
		</listitem>

		<listitem id="apolar-calcforce">
			<cmdsynopsis>
				<command>calcforce</command>
				<arg choice="req"> <replaceable>flag</replaceable> </arg>
			</cmdsynopsis>
			<para>
				This optional keyword controls apolar force output.
				<note>
					<para> Note that this option must be used consistently for all
						calculations that will appear in subsequent 
						<link linkend="print"><command>PRINT</command></link> statements.
						For example, if the statement <literal>print force 1 - 2
							end</literal> appears in the input file, then both calculations 1
						and 2 must have <command>calcforce</command> keywords present with
						the same values for <replaceable>flag</replaceable>.
					</para>
				</note>
				<variablelist>
					<varlistentry>
						<term> <replaceable>flag</replaceable> </term>
						<listitem>
							<para>Specify the types of force values to be returned:
								<variablelist>
									<varlistentry>
										<term>no</term>
										<listitem>
											<para>(Deprecated) don't calculate any forces.</para>
										</listitem>
									</varlistentry>
									<varlistentry>
										<term>total</term>
										<listitem>
											<para>Calculate and return total apolar forces for the entire molecule.</para>
										</listitem>
									</varlistentry>
									<varlistentry>
										<term>comps</term>
										<listitem>
											<para>Calculate and return total apolar forces for the entire molecule as well as force components for each atom.</para>
										</listitem>
									</varlistentry>
								</variablelist>
							</para>
						</listitem>
					</varlistentry>
				</variablelist>
			</para>
		</listitem>

		<listitem id="apolar-dpos">
			<cmdsynopsis>
				<command>dpos</command>
				<arg
					choice="req"><replaceable>displacement</replaceable></arg>
			</cmdsynopsis>
			<para>This is the displacement used for
				finite-difference-based calculations of surface
				area derivatives.  I know:  this is a terrible
				way to calculate surface area derivatives --
				we're working on replacing it with an analytic
				version.  In the meantime, please use this
				parameter with caution.  
			</para>	
			<important>
				<para>This parameter is very dependent on <link linkend="apolar-sdens">sdens</link>; e.g., smaller values of <literal>dpos</literal> require larger values of <link linkend="apolar-sdens">sdens</link>.</para> 
			</important>
			<variablelist>
				<varlistentry>
					<term><replaceable>dispalcement</replaceable></term>
					<listitem>
						<para>Finite difference
							displacement for force
							(surface area
							derivative) 
							calculations in units
							of &Aring;.  </para>
					</listitem>
				</varlistentry>
			</variablelist>
		</listitem>

		<listitem id="apolar-gamma">
			<cmdsynopsis>
				<command>gamma</command>
				<arg choice="req"> <replaceable>value</replaceable> </arg>
			</cmdsynopsis>
			<para>
				The coefficient (surface tension) for solvent-accesisble surface area
				(SASA) models of apolar solvation.    This term
				can be set to zero to eliminate SASA
				contributions to the apolar solvation
				calculations.
				<variablelist>
					<varlistentry>
						<term><replaceable>value</replaceable></term>
						<listitem>
							<para>SASA-based apolar coefficient (in kJ/mol/&Aring;).</para>
						</listitem>
					</varlistentry>
				</variablelist>
			</para>
		</listitem>

		<!--
		FINISH:  this term should be added back, I think.
		<listitem id="gcent">
			<cmdsynopsis>
				<command>gcent</command>
				<group choice="req">
					<arg choice="plain">mol <replaceable>id</replaceable></arg>
					<arg choice="plain"><replaceable>xcent ycent zcent</replaceable></arg>
				</group>
			</cmdsynopsis>
			<para>Specify the center of the grid based on a molecule's center or
				absolute coordinates. The arguments for this keyword are:
				<variablelist>
					<varlistentry>
						<term>mol <replaceable>id</replaceable></term>
						<listitem>
							<para>Center the grid on molecule with ID
								<replaceable>id</replaceable>; as assigned in the 
								<link linkend="read"><command>READ</command></link> section.
								Molecule IDs are assigned in the order they're read, starting
								at 1. 
							</para>
						</listitem>
					</varlistentry>
					<varlistentry>
						<term><replaceable>xcent ycent zcent</replaceable></term>
						<listitem>
							<para>The coordinates (in &Aring;) at which the grid is
								centered.  Based on the PDB coordinate frame.</para>
						</listitem>
					</varlistentry>
				</variablelist>
			</para>
		</listitem>
		-->

		<listitem id="apolar-grid">
			<cmdsynopsis>
				<command>grid</command>
				<arg choice="req"><replaceable>hx hy hz</replaceable></arg>
			</cmdsynopsis>
			<para>Specify the quadrature grid spacing for volume integral calculations.
				<variablelist>
					<varlistentry>
						<term><replaceable>hx hy hz</replaceable></term>
						<listitem>
							<para>Quadrature spacing in the x-, y-, and z-directions in &Aring;.</para>
						</listitem>
					</varlistentry>
				</variablelist>
			</para>
		</listitem>

		<listitem id="apolar-mol">
			<cmdsynopsis>
				<command>mol</command>
				<arg choice="req"><replaceable>id</replaceable></arg>
			</cmdsynopsis>
			<para>Specify the molecule for which the apolar
				calculation is to be performed.  IDs are based
				on the order in which molecules are read by 
				<link linkend="read-mol"><command>read mol</command></link> statements,
				starting from 1.
				<variablelist>
					<varlistentry>
						<term><replaceable>id</replaceable></term>
						<listitem>
							<para>The ID of the
								molecule for
								which the
								apolar
								calculation is
								to be
								performed.</para>
						</listitem>
					</varlistentry>
				</variablelist>
			</para>
		</listitem>

		<listitem id="apolar-press">
			<cmdsynopsis>
				<command>press</command>
				<arg choice="req"><replaceable>solvent pressure</replaceable></arg>
			</cmdsynopsis>
			<para>Specify the solvent pressure in kJ
				mol<superscript>-1</superscript>
				&Aring;<superscript>-3</superscript>. This
				coefficient multiplies the volume term of the
				apolar model discussed above and can be set to
				zero to eliminate volume contributions to the
				apolar solvation calculation.</para>
			<variablelist>
				<varlistentry>
					<term><replaceable>solvent pressure</replaceable></term>
					<listitem><para>Solvent pressure
							(in kJ
							mol<superscript>-1</superscript>
							&Aring;<superscript>-3</superscript>)</para></listitem>
				</varlistentry>
			</variablelist>
		</listitem>

		<listitem id="apolar-sdens">
			<cmdsynopsis>
				<command>sdens</command>
				<arg choice="req"><replaceable>surface
						discretization density</replaceable></arg>
			</cmdsynopsis>
			<para>Specify the number of grid points per square-angstrom to use 
				in surface calculations (e.g., molecular
				surface, solvent accesible surface). Ignored when srad is 0.0 (see 
				<link linkend="apolar-srad"><command>srad</command></link>) or srfm is 
				spl2 (see <link linkend="apolar-srfm"><command>srfm</command></link>).
				Users beware:  there is a direct correlation
				between the value used for the sphere density,
				the accuracy of the results, and the APBS
				calculation time.
				<variablelist>
					<varlistentry>
						<term><replaceable>surface
								discretization density</replaceable></term>
						<listitem>
							<para>Surface sphere density (in grid points/&Aring;<superscript>2
							</superscript>).</para>
						</listitem>
					</varlistentry>
				</variablelist>
			</para>
		</listitem>

		<listitem id="apolar-srad">
			<cmdsynopsis>
				<command>srad</command>
				<arg choice="req"><replaceable>radius</replaceable></arg>
			</cmdsynopsis>
			<para>Specify the radius of the solvent molecules; this parameter is used
				to define various solvent-related surfaces and
				volumes (see <link
					linkend="apolar-srfm"><command>srfm</command></link>).
				This value is usually set to 1.4 &Aring; for
				water.
				<variablelist>
					<varlistentry>
						<term><replaceable>radius</replaceable></term>
						<listitem>
							<para>Solvent radius (in &Aring;).</para>
						</listitem>
					</varlistentry>
				</variablelist>
			</para>
		</listitem>

		<listitem id="apolar-swin">
			<cmdsynopsis>
				<command>swin</command>
				<arg choice="req"><replaceable>win</replaceable></arg>
			</cmdsynopsis>
			<para>Specify the size of the support (i.e., the rate of change) for
				spline-based surface definitions 
				(see <link linkend="apolar-srfm"><command>srfm</command></link>).  
				Usually 0.3 &Aring;.
				<variablelist>
					<varlistentry>
						<term><replaceable>win</replaceable></term>
						<listitem>
							<para>Spline window (in &Aring;).</para>
						</listitem>
					</varlistentry>
				</variablelist>
			</para>
		</listitem>

		<listitem id="apolar-srfm">
			<cmdsynopsis>
				<command>srfm</command>
				<arg choice="req"><replaceable>flag</replaceable></arg>
			</cmdsynopsis>
			<para>
				Specify the model used to construct the
				solvent-related surface and volume
				<note> <para>Under construction:  we're in the
						process of adding additional
						surface definitions.</para>
				</note>
				<variablelist>
					<varlistentry>
						<term><replaceable>flag</replaceable></term>
						<listitem>
							<para>
								The
								surface/volume model:
								<variablelist>
									<varlistentry>
										<term>sacc</term>
										<listitem>
											<para>Solvent-accessible
												(also
												called
												"probe-inflated")
												surface
												and
												volume.
											</para>
										</listitem>
									</varlistentry>
								</variablelist>
							</para>
						</listitem>
					</varlistentry>
				</variablelist>
			</para>
		</listitem>

		<listitem id="apolar-temp">
			<cmdsynopsis>
				<command>temp</command>
				<arg choice="req"> <replaceable>T</replaceable> </arg>
			</cmdsynopsis>
			<para>Temperature for calculation.
				<variablelist>
					<varlistentry>
						<term><replaceable>T</replaceable></term>
						<listitem>
							<para>Temperature (in K)</para>
						</listitem>
					</varlistentry>
				</variablelist>
			</para>
		</listitem>


	</itemizedlist>


</sect3>