SCRF

This keyword requests that a calculation be performed in the presence of a solvent by placing the solute in a cavity within the solvent reaction field.

The Polarizable Continuum Model (PCM) using the integral equation formalism variant (IEFPCM) is the default SCRF method. This method creates the solute cavity via a set of overlapping spheres. It was initially devised by Tomasi and coworkers and Pascual-Ahuir and coworkers [Miertus81, Miertus82, Pascual-Ahuir94], and it has been further developed in Gaussian by the Tomasi, Barone and Mennucci groups as well as Gaussian, Inc. researchers and collaborators [Cossi96, Barone97, Cances97, Mennucci97, Mennucci97a, Barone98, Cossi98, Barone98a, Cammi99, Cossi99, Tomasi99, Cammi00, Cossi00, Cossi01, Cossi01a, Cossi02, Cossi03, Cammi09, Cammi10, Scalmani10, Lipparini10, Caricato12b]. This model corresponds to SCRF=PCM. See [Tomasi05] for a review. The model of Chipman [Chipman00] is closely related to this method [Cances01].

Other available models are IPCM, which uses a static isodensity surface for the cavity [Foresman96], the Self-Consistent Isodensity PCM (SCIPCM) model [Foresman96], and the Onsager model [Kirkwood34, Onsager36, Wong91, Wong91a, Wong92, Wong92a], which places the solute in a spherical cavity within the solvent reaction field.

In Gaussian 16, we use a continuous surface charge formalism that ensures continuity, smoothness and robustness of the reaction field, which also has continuous derivatives with respect to atomic positions and external perturbing fields [Scalmani10]. This is achieved by expanding the apparent surface charge that builds up at the solute-solvent interface in terms of spherical Gaussian functions located at each surface element in which the cavity surface is discretized. Discontinuities in the surface derivatives are removed by effectively smoothing the regions where the spheres intersect. This formalism, initially proposed in 1999 by Karplus and York for the conductor screening model [York99], never received the attention it deserved. We developed and generalized it within the framework of the PCM family of solvation methods in G09, and it is the default method for building the solute's cavity and computing the reaction field.

The PCM method in Gaussian 16 includes an external iteration procedure whereby the program computes the energy in solution by making the solvent reaction field self-consistent with the solute electrostatic potential (the latter being generated from the computed electron density with the specified model chemistry) [Improta06, Improta07]. The difference with the standard approach (based on the variational approach or linear response theory) can be illustrated with MP2. The default procedure computes the solvent effect on the SCF density and then applies MP2 perturbation, while the external iteration approach computes the solvent effect self-consistently with respect to the MP2 density. While this technique is of primary interest for studying excited state processes such fluorescence, it can also be used for ground state calculations with theoretical methods that provide gradients: e.g. post-SCF methods. Use the ExternalIteration option to specify this method.

Solvation and Excited States

There are two basic approaches available for modeling excited states in solution:

• Computing the lowest excited states in the solvent environment. This approach adds SCRF to a normal excited state calculation such as TD or CIS. This technique employs a linear response formalism by adding the necessary terms to the excited state method equations (thereby including the solvent effects on the excited states) [Cammi00, Cossi01]. The geometry of a specific excited state can be optimized in solution with CIS or TD [Scalmani06].
• A single excited state can be modeled via a state-specific approach. In this case, the program computes the energy in solution by making the electrostatic potential generated by the excited state density self consistent with the solvent reaction field [Improta06, Improta07], using the external iteration technique.

For excited state calculations in solution, there is a distinction between equilibrium and non-equilibrium calculations. The solvent responds in two different ways to changes in the state of the solute: it polarizes its electron distribution, which is a very rapid process, and the solvent molecules reorient themselves (e.g., by a rotation), a much slower process. An equilibrium calculation describes a situation where the solvent had time to fully respond to the solute (in both ways), e.g., a geometry optimization (a process that takes place on the same time scale as molecular motion in the solvent). A non-equilibrium calculation is appropriate for processes which are too rapid for the solvent to have time to fully respond, e.g. a vertical electronic excitation.

Equilibrium solvation is the default for CIS and TD-DFT excited state geometry optimizations. Non-equilibrium is the default for CIS and TD-DFT energies using the default PCM procedure, and equilibrium is the default for calculations using the external iteration approach (SCRF=ExternalIteration). See the examples for the method for computing non-equilibrium external iteration calculations.

For EOM-CCSD calculations in solution, the solvation approaches of Cammi and Caricato are available [Cammi09, Cammi10, Caricato12b]. The PTED method is available with the PTED option. Other methods discussed in [Caricato12b] are also available via IOp(9/116).

By default, CASSCF PCM [Cossi99] calculations correspond to equilibrium calculations with respect to the solvent reaction field/solute electronic density polarization process. Calculation of non equilibrium solute-solvent interaction involving two different electronic states (e.g. the initial and final states of a vertical transition) can be performed using the NonEq=type PCM keyword, in two separate job steps (see PCM in the Input section).

Keywords and options specifying details for a PCM calculation (i.e., the default SCRF=PCM or SCRF=CPCM) may be specified in an additional blank-line terminated input section provided that the Read option is also specified. Keywords within this section follow general Gaussian input rules. The available keywords are listed in a separate subsection following the examples.

For the Onsager model (SCRF=Dipole), the solute radius in Angstroms and the dielectric constant of the solvent are read as two free-format real numbers on one line from the input stream. A suitable solute radius is computed by a gas-phase molecular volume calculation (in a separate job step); see the discussion of the Volume keyword.

For the IPCM and SCIPCM models, the input consists of a line specifying the dielectric constant of the solvent and an optional isodensity value (the default for the latter is 0.0004).

Specifying the Solvent

Solvent=item

Selects the solvent in which the calculation is to be performed. Note that the solvent may also be specified in the input stream in various ways for the different SCRF methods. If unspecified, the solvent defaults to water. Item is a solvent name chosen from the list at the end of this section.

Selecting the SCRF Method

PCM

Performs a reaction field calculation using the integral equation formalism model (IEFPCM). This is the default. Some details of the formalism and the implementation have changed with respect to Gaussian 03, as described in [Scalmani10]. IEFPCM is a synonym for PCM.

When PCM is used for an anisotropic or ionic solvent, then items in the PCM input section must be used to select the anisotropic and ionic dielectric models for these types of solvents, using the Read option. The continuous surface charge formalism is also not available with such solvents, and no derivatives can be computed.

CPCM

Performs a PCM calculation using the CPCM polarizable conductor calculation model [Barone98, Cossi03].

Dipole

Performs an Onsager model reaction field calculation.

IPCM

Performs an IPCM model reaction field calculation. Isodensity is a synonym for IPCM.

SCIPCM

Performs an SCIPCM model reaction field calculation, i.e. the SCRF calculation uses a cavity determined self-consistently from an isodensity surface.

SMD Model

SMD

Do an IEFPCM calculation with radii and non-electrostatic terms for Truhlar and coworkers' SMD solvation model [Marenich09]. This is the recommended choice for computing ΔG of solvation, which accomplished by performing gas phase and SCRF=SMD calculations for the system of interest and taking the difference the resulting energies.

PCM Non-Equilibrium Solvation

NonEquilibrium=action

Save or retrieve data for non-equilibrium solvation. Action is one of the following:

• Save or Write: Save the slow/inertial charges in the checkpoint file (from which they will be retrieved in a subsequent non-equilibrium solvation calculation).
• Read or Load: Read the slow/inertial charges for use in the current non-equilibrium solvation calculation.
• CCSave or CCWrite: Save the slow/inertial correlation charges for use in a subsequent non-equilibrium solvation coupled cluster calculation.
• CCRead or CCLoad: Retrieve the slow/inertial correlation charges for use in the current non-equilibrium solvation coupled cluster calculation.

External Iteration PCM

ExternalIteration

Does a self-consistent PCM calculation performing an external iteration through Link 124. This approach computes the energy in solution by making the solute's electrostatic potential self-consistent with the solvent reaction field [Improta06, Improta07]. ExternalIteration is available only for energy calculations. SelfConsistent and SC are synonyms for this option.

1stVac

Do the first iteration in an external iteration PCM calculation in solution. 1stVac is equivalent to DoVacuum, which is now deprecated.

1stPCM

Do not do the first iteration in an external iteration PCM calculation in solution. 1stPCM is equivalent to SkipVacuum and NoVacuum, which are now deprecated.

Restart

Restarts a PCM external iteration calculation from the checkpoint file.

IEFPCM and CPCM Other Options

SolventAccessibleSurface

For PCM, use a cavity representing the solvent-accessible surface. Only suitable for single-point calculations, but useful for cases with unusual cavities, snapshots from MD with explicit solvent, etc. SCRF=SAS is a synonym for this option.

AsymmetricIEFPCM

Perform asymmetric isotropic IEFPCM rather than the default of symmetric isotropic IEFPCM. AsymmetricIEFPCM was the default in Gaussian 09.
SCRF=AIEFPCM is a synonym for this option. Not valid with CPCM.

PTED

Use the perturbation theory and density approach (PTED) to PCM-CCSD coupling [Cammi09, Caricato12b] for an EOM-CCSD calculation in solution. Other schemes discussed in [Caricato12b] are available via IOp(9/116).

CorrectedLinearResponse

Do a state-specific correction to the energy of a CIS/RPA/TD-DFT SCRF excited state, according to [Caricato06]. CorrectedLR is a synonym for this option.

Read

Indicates that a separate section of keywords and options providing calculation parameters should be read from the input stream. This must be specified for anisotropic and ionic solvents.

Checkpoint

Retrieves the SCRF information from the checkpoint file.

Modify

Retrieves the SCRF information from the checkpoint file, and also reads modifications from the input stream.

ONIOMPCM=k

Performs an ONIOM calculation in solution [Vreven01, Mo04] according to the scheme selected by the code letter k, for which these are the valid values:

G09Defaults

Sets defaults for PCM solvation back to those used in Gaussian 09.

G03Defaults

Modify the PCM defaults in order to reproduce the results of a Gaussian 03 PCM calculation as closely as possible. Note that perfect agreement is not always possible due to improvements in the program.

Onsager (SCRF=Dipole) Model Options

A0=val

Sets the value for the solute radius a₀ in the route section (rather than reading it from the input stream of an SCRF=Dipole calculation). If this option is included, then Solvent or Dielectric must also be included.

Dielectric=val

Sets the value for the dielectric constant of the solvent. This option overrides Solvent if both are specified.

IPCM Model Options

GradVne

Use Vne basins for the numerical integration.

GradRho

Use density basins for the numerical integration. The job may fail if non-nuclear attractors are present.

SCIPCM Model Options

UseDensity

Force the use of the density matrix in evaluating the density.

UseMOs

Force the use of MOs in evaluating the density.

GasCavity

Use the gas phase isodensity surface to define the cavity rather than solving for the surface self-consistently. This is mainly a debugging option.

Save/Retrieve PCM Charges

SaveQ

Write the PCM charges on the checkpoint file. SaveQ can be specified together with LoadQ. WriteQ is a synonym for this option.

LoadQ

Read the PCM charges on the checkpoint file. Note that the molecular geometry and the cavity must match exactly to use the saved charges. SaveQ can be specified together with LoadQ. ReadQ is a synonym for this option.

Produce Input for COSMO/RS

COSMORS

Produces the data file used by COSMO/RS and other programs.

The following table details the availability of the various SCRF=PCM calculation types by theoretical method:

^aFor example,Freq=Raman, ROA or VCD; ^bComputed via SCF MO polarization; ^cRaman intensities are computed numerically (i.e., as with Freq=NRaman); ^dUsing the linear response approach; ^eNumerical frequencies only.

CASSCF frequencies with PCM solvation must be done numerically using Freq=Numer.

Restarting SCRF Calculations. SCRF=ExternalIteration and SCRF=IPCM jobs can be restarted from the read-write file by using the Restart option. SCRF=SCIPCM calculations that fail during the SCF iterations should be restarted via the SCF=Restart keyword.

Non-Default Methods. The IPCM model is available for HF, DFT, MP2, MP3, MP4(SDQ), QCISD, CCD, CCSD, CID, and CISD energies only. The SCIPCM model is available for HF and DFT energies and optimizations and numerical frequencies. The Onsager (SCRF=Dipole) model is available for HF, DFT, MP2, MP3, MP4(SDQ), QCISD, CCD, CCSD, CID, and CISD energies, and for HF and DFT optimizations and frequency calculations. However, the Opt Freq keyword combination may not be used in SCRF=Dipole calculations.

SCF, Volume

PCM Energy. In general, energy output from the default SCRF method appears in the normal way within the output file. For example, here are the sections of the output file containing the predicted energy from a Hartree-Fock and from an MP2 PCM calculation:

 Hartree-Fock SCRF calculation:
 SCF Done:  E(RHF) =  -99.4687828290     A.U. after    8 cycles
             Convg  =    0.2586D-08             -V/T =  2.0015
 
 MP2 SCRF calculation:			
 E2 =    -0.1192799427D+00  EUMP2 =    -0.99584491345297D+02

The predicted energy in solution includes all computed corrections (unlike in Gaussian 03 output).

Additional output lines may appear when various PCM options are included. For example, the following output is produced by an HF SCRF=SMD calculation:

 SCF Done:  E(RHF) =  -99.4687828290     A.U. after    8 cycles
             Convg  =    0.2586D-08             -V/T =  2.0015
 SMD-CDS (non-electrostatic) energy             (kcal/mol) =       0.54
 (included in total energy above)

For external iteration SCRF calculations, the final energy is computed by Link 124, which controls the external iteration, and is reported in a separate output section, which will appear very near the end of the output file, as in the following example:

 --------------------------------------------------------------------
 Self-consistent PCM results
 ===========================
 <psi(f)|   H    |psi(f)>                     (a.u.) =     -99.577537(A)
 <psi(f)|H+V(f)/2|psi(f)>                     (a.u.) =     -99.584002(B)
 (Polarized solute)-Solvent               (kcal/mol) =      -4.06(C)
 --------------------------------------------------------------------
 Partition over spheres:
 Sphere  on Atom  Surface  Charge   GEl     GCav    GDR
    1      H1      15.27  -0.157   -2.36    0.00    0.00
    2      F2      32.58   0.157   -1.70    0.00    0.00
 --------------------------------------------------------------------
 Predicted energy value for external iteration and state-specific SCRF calculations
 After PCM corrections, the energy is  -99.5840023899     a.u. 
 --------------------------------------------------------------------

Line (A) reports the energy computed using the polarized solute wavefunction and the gas phase Hamiltonian, line (B) reports energy computed using the polarized solute wavefunction and the Hamiltonian in solution, line (C) reports the interaction energy between the polarized solute and the solvent, which corresponds to the integral <Ψ(f)|V(f)/2|Ψ(f)> (in kcal/mol), and the final line reports the predicted energy incorporating all PCM corrections.

Fluorescence example: Emission (Fluorescence) from First Excited State (n→π*) of Acetaldehyde

Here we study the cycle:

Acetaldehyde Excitation and Emission Cycle

The primary process of interest is the emission, but this example shows how to study the complete cycle including the solvent effects.

Step 1: Ground state geometry optimization and frequencies (equilibrium solvation). This is a standard Opt Freq calculation on the ground state including PCM equilibrium solvation.

%chk=01-ac
# B3LYP/6-31+G(d,p) Opt Freq SCRF=(Solvent=Ethanol) 

Acetaldehyde ground state

0 1
C
C,1,RA
X,2,1.,1,A
O,2,RB,3,A,1,180.,0
X,1,1.,2,90.,3,0.,0
H,1,R1,2,A1,5,0.,0
H,1,R23,2,A23,5,B23,0
H,1,R23,2,A23,5,-B23,0
H,2,R4,1,A4,3,180.,0
 
RA=1.53643
RB=1.21718
R1=1.08516
R23=1.08688
R4=1.10433
A=62.1511
A1=110.51212
A23=109.88119
A4=114.26114
B23=120.56468

Here is the energy of the ground state optimized geometry in solution:

SCF Done:  E(RB3LYP) =  -153.851761719     A.U. after    1 cycles

Step 2: Vertical excitation with linear response solvation. This is a TD-DFT calculation of the vertical excitation, therefore at the ground state equilibrium geometry, with the default solvation: linear response, non-equilibrium. We perform a single-point TD-DFT calculation, which defaults to non-equilibrium solvation. The results of this job will be used to identify which state or states are of interest and their ordering. These results give a reasonable description of the solvation of the excited state, but not quite as good as that from a state-specific solvation calculation. In this case, we see that the n→π* state is the first excited state. Next, we will use the state-specific method to produce a better description of the vertical excitation step.

%oldchk=01-ac
%chk=02-ac
# B3LYP/6-31+G(d,p) TD=NStates=6 SCRF=(Solvent=Ethanol) Geom=Check Guess=Read

Acetaldehyde: linear response vertical excited states

0 1

The vertical excitation (absorption) to first excited state from the non-equilibrium solvation linear response calculation:

Excited State   1:      Singlet-A"     4.3767 eV  283.28 nm  f=0.0000  <S**2>=0.000

Thus, the ground state to first excited state absorption is at 283.28 nm, computed via the linear-response approach.

Step 3: State-specific solvation of the vertical excitation. This will require two job steps: first the ground state calculation is done, specifying the NonEquilibrium=Save option, in order to store the information about non-equilibrium solvation based on the ground state. Second, the actual state-specific calculation is done, reading in the necessary information for non-equilibrium solvation using NonEquilibrium=Read option, and specifying the checkpoint file from Step 1:

%oldchk=01-ac
%chk=03-ac
# B3LYP/6-31+G(d,p) SCRF=(Solvent=Ethanol,NonEquilibrium=Save) 
  Geom=Check Guess=Read 

Acetaldehyde: prepare for state-specific non-eq solvation
by saving the solvent reaction field from the ground state

0 1

--link1--
%chk=03-ac
# B3LYP/6-31+G(d,p) TD(NStates=6,Root=1) Geom=Check Guess=Read
  SCRF=(Solvent=Ethanol,ExternalIteration,NonEquilibrium=Read)

Acetaldehyde: read non-eq solvation from ground state and 
compute energy of the first excited with the state-specific method

0 1

Here is the energy of first excited state—at the ground state optimized geometry—from the non-equilibrium solvation state-specific calculation:

After PCM corrections, the energy is  -153.687679826     a.u.

Subtracting this energy from the ground state energy (from step 1) gives the ground state to first excited state absorption including the state-specific solvation correction: at 277.69 nm.

Step 4: Relaxation of the excited state geometry. Next, we perform a TD-DFT geometry optimization, with equilibrium, linear response solvation, in order to find the minimum energy point on the excited state potential energy surface. Since this is a TD-DFT optimization, the program defaults to equilibrium solvation. As is typical of such cases, the molecule has a plane of symmetry in the ground state but the symmetry is broken in the excited state, so the ground state geometry is perturbed slightly to break symmetry at the start of the optimization. We retrieve the geometry and other data from the checkpoint file from Step 2:

%oldchk=02-ac
%chk=04-ac
# B3LYP/6-31+G(d,p) TD=(Read,NStates=6,Root=1) SCRF=(Solvent=Ethanol) 
  Geom=Modify Guess=Read Opt=ReadFC

Acetaldehyde: excited state opt
Modify geometry to break Cs symmetry 
since first excited state is A"

0 1

4 1 2 3 10.0
5 1 2 7 -50.0

Here are the results for the first excited state after the geometry optimization of first excited state in solution (equilibrium geometry):

Excited State   1: Singlet-A    3.2074 eV  386.55 nm  f=0.0013  <S**2>=0.000  12 -> 13    0.70615  
This state for optimization and/or second-order correction.  
Total Energy, E(TD-HF/TD-KS) =  -153.705918726

Step 5: Vibrational frequencies of the excited state structure. Now we run a frequency calculation to verify that the geometry located in step 4 is a minimum. The results could also be used as part of a Franck-Condon calculation if desired. This is a numerical frequency calculation.

%oldchk=04-ac
%chk=05-ac
# B3LYP/6-31+G(d,p) TD=(Read,NStates=6,Root=1) Freq
  SCRF=(Solvent=Ethanol) Geom=Check Guess=Read 

Acetaldehyde excited state freq

0 1

The frequency calculation is used to confirm that the geometry optimized in Step 4 is a minimum on the excited state potential energy surface.

Step 6: Emission state-specific solvation (part 1). This step does state-specific equilibrium solvation of the excited state at its equilibrium geometry, writing out the solvation data for the next step via the NonEquilibrium=Save option.

%oldchk=05-ac
%chk=06-ac
# B3LYP/6-31+G(d,p) TD=(Read,NStates=6,Root=1) Geom=Check Guess=Read
  SCRF=(Solvent=Ethanol,ExternalIteration,NonEquilibrium=Save)

Acetaldehyde emission state-specific solvation
at first excited state optimized geometry

0 1

Here is the energy of first excited state—at its optimized geometry—from the equilibrium solvation state-specific calculation:

After PCM corrections, the energy is  -153.707148980     a.u.

Step 7: Emission to final ground state (part 2). Finally, we compute the ground state energy with non-equibrium solvation, at the excited state geometry and with the static solvation from the excited state.

%oldchk=06-ac
%chk=07-ac
# B3LYP/6-31+G(d,p) SCRF=(Solvent=Ethanol,NonEquilibrium=Read)
  Geom=Check Guess=Read

Acetaldehyde: ground state non-equilibrium
at excited state geometry.

0 1

Here is the energy of ground state from a non-equilibrium solvation calculation in solution, using the first excited state optimized geometry and the solvent reaction field in equilibrium with the first excited state density):

SCF Done:  E(RB3LYP) =  -153.822024722     A.U. after   10 cycles

The difference between the energies from steps 6 and 7 gives the vertical emission energy. In this case, the first excited state to ground state emission, including the state-specific solvation correction, is at 396.63 nm.

Steps 1, 2, and 4 would be sufficient to compute the excitation and emission energies in the gas-phase (along with step 5 to confirm the nature of stationary point). They are not sufficient when solvent effects are included because the energies computed in step 4 correspond to the ground state solvent reaction field, while the emission takes place in the reaction field created in response to the excited state charge distribution. This is what is accounted for properly in steps 6 and 7.

If the band shape is to be calculated, then in the gas phase one would simply run a calculation with Freq=(ReadFC,FC,Emission), giving the checkpoint file from step 1 as the main checkpoint file for the job, and providing the name of the checkpoint file from step 5 in the input stream to specify the other state. For the solvated band shape, one must do Freq=(ReadFC,FC,Emission,ReadFCHT) using the checkpoint files for steps 1 and 5, but also providing the state-specific emission energy in the input section for the Franck-Condon calculation.

Additional Input for PCM Calculations

Additional input keywords may be specified for PCM SCRF calculations. They are placed in a separate input section, terminated as usual by a blank line, as in this example:

The PCM input section ends as usual with a blank line.

The following keywords are available for controlling PCM calculations (arranged in groups of related items).

Defining Solvent Parameters

The solvent for the PCM calculation is generally specified using the normal Solvent option to the SCRF keyword. You can use the following keywords to override some default values for known solvents.

Unspecified parameters default to the values for the solvent specified with the Solvent option (or to water if this option is omitted).

Calculation Method Variations

Anisotropic and Ionic Solvents

Specifying the Molecular Cavity

By default, the program builds up the cavity using the UFF radii, which places a sphere around each solute atom, with the radii scaled by a factor of 1.1. There are also three United Atom (UA) models available.

The cavity can be extensively modified in the PCM input section: changing sphere parameters and the general cavity topology, adding extra spheres to the cavity built by default, and so on. The whole molecular cavity can be also provided by the user in the input section.

Radii=model: Indicates the topological model and/or the set of atomic radii used. Available models and sets are:

• UFF: Uses radii from the UFF force field. Hydrogens have individual spheres (explicit hydrogens). This is the default.
• UA0:Uses the United Atom Topological Model applied on atomic radii of the UFF force field for heavy atoms. Hydrogens are enclosed in the sphere of the heavy atom to which they are bonded. This was the default in Gaussian 03.
• UAHF: Uses the United Atom Topological Model applied on radii optimized for the HF/6-31G(d) level of theory.
• UAKS: Uses the United Atom Topological Model applied on radii optimized for the PBE1PBE/6-31G(d) level of theory.
• Pauling: Uses the Pauling (actually Merz-Kollman) atomic radii (uses explicit hydrogens).
• Bondi: Uses the Bondi atomic radii (uses explicit hydrogens).

Surface=type: Specify the type of molecular surface representing the solute-solvent boundary. Available options are:

• VDW: Van der Waals surface. Uses atomic radii (scaled) and skips the generation of “added spheres” to smooth the surface. This is the default.
• SES: Solvent Excluding Surface. The surface is generated by the atomic or group spheres and by the spheres created automatically to smooth the surface (“added spheres”). This was the default in Gaussian 03.
• SAS: Solvent Accessible Surface. The radius of the solvent is added to the unscaled radii of atoms and/or atomic groups.

ModifySph: Alters parameters for one or more spheres. The modified spheres can be indicated in the PCM input in lines following this keyword having the following format:

   atom radius [alpha]

where atom is the atom number or element type.

ExtraSph=N: Adds N user-defined spheres to the cavity. Parameters of the spheres can be specified in lines following this keyword using the following format:

   X Y Z radius [alpha]

where X,Y,Z are the Cartesian coordinates in the standard orientation.

NSph=N: The cavity is built just from the N spheres provided by the user, specified on lines of the following format:

   atom_number radius [alpha] —or— X Y Z radius [alpha]

where X,Y,Z are the Cartesian coordinates in the standard orientation. Specifying spheres by atom number mimics standard cavity behavior, while specifying Cartesian produces a fixed cavity which does not move with the structure.