howto:resp
Differences
This shows you the differences between two versions of the page.
Both sides previous revisionPrevious revisionNext revision | Previous revisionNext revisionBoth sides next revision | ||
howto:resp [2015/12/02 16:53] – [Example input files] dgolze | howto:resp [2015/12/08 12:35] – [Fitting the variance (REPEAT method)] dgolze | ||
---|---|---|---|
Line 16: | Line 16: | ||
\end{equation} | \end{equation} | ||
For more details see: | For more details see: | ||
- | * [[ | + | [[doi>10.1021/ |
==== Periodic fitting ==== | ==== Periodic fitting ==== | ||
Line 24: | Line 24: | ||
\end{equation} | \end{equation} | ||
where $g_a$ is a Gaussian function centered at atom $a$. The periodic fitting is embedded in a Gaussian and plane waves (GPW) framework and described in detail in | where $g_a$ is a Gaussian function centered at atom $a$. The periodic fitting is embedded in a Gaussian and plane waves (GPW) framework and described in detail in | ||
- | * [[ | + | [[doi>10.1039/ |
- | In the periodic case, CP2K offers also the possibility to fit the variance of the potential instead of the absolute values, see below. | + | In the periodic case, CP2K offers also the possibility to fit the variance of the potential instead of the absolute values, see [[resp# |
===== Basic input ===== | ===== Basic input ===== | ||
- | The RESP fitting is a post-SCF step and included as a subsection of the [[http:// | + | The RESP fitting is a post-SCF step and included as a subsection of the [[inp>FORCE_EVAL/ |
<code cp2k> | <code cp2k> | ||
Line 41: | Line 41: | ||
With this basis setup, the following defaults are employed: | With this basis setup, the following defaults are employed: | ||
* All points outside the van der Waals radii (taken from the Cambridge database) of the atoms are included | * All points outside the van der Waals radii (taken from the Cambridge database) of the atoms are included | ||
- | * The total charge of the system as defined in [[http:// | + | * The total charge of the system as defined in [[inp>FORCE_EVAL/ |
- | * All atoms except the hydrogens are weakly restrained to zero, i.e. [[http:// | + | * All atoms except the hydrogens are weakly restrained to zero, i.e. [[inp>FORCE_EVAL/ |
===== Sampling of fit points ===== | ===== Sampling of fit points ===== | ||
Line 55: | Line 55: | ||
&END RESP | &END RESP | ||
</ | </ | ||
- | For better visualization it is recommended to center the coordinates of the systems using [[http:// | + | For better visualization it is recommended to center the coordinates of the systems using [[inp>FORCE_EVAL/ |
==== Sphere sampling ==== | ==== Sphere sampling ==== | ||
< | < | ||
This type of sampling is employed for isolated molecules and porous periodic structures suchs as metal-organic frameworks (MOFs). | This type of sampling is employed for isolated molecules and porous periodic structures suchs as metal-organic frameworks (MOFs). | ||
All grid points within a given spherical shell around the atom are included in the fitting, | All grid points within a given spherical shell around the atom are included in the fitting, | ||
- | For the vdW radii, the values from the Cambridge Structural Database '' | + | For the vdW radii, the values from the Cambridge Structural Database '' |
* r$_{\mathrm{min}}$ = AUTO_RMIN_SCALE $\cdot$ vdW_radius | * r$_{\mathrm{min}}$ = AUTO_RMIN_SCALE $\cdot$ vdW_radius | ||
* r$_{\mathrm{max}}$ = AUTO_RMAX_SCALE $\cdot$ vdW_radius | * r$_{\mathrm{max}}$ = AUTO_RMAX_SCALE $\cdot$ vdW_radius | ||
Line 107: | Line 107: | ||
===== Constraints ===== | ===== Constraints ===== | ||
- | A constraint on the total charge of the system is introduced by the keyword [[http:// | + | A constraint on the total charge of the system is introduced by the keyword [[inp>FORCE_EVAL/ |
<code cp2k> | <code cp2k> | ||
& | & | ||
Line 116: | Line 116: | ||
where '' | where '' | ||
The definition of more elaborate constraints is also possible. The constraints are always linear following the formula | The definition of more elaborate constraints is also possible. The constraints are always linear following the formula | ||
- | $\sum_i^{n\_list}c_iq_i=t$. The sum is running over the atoms given in '' | + | $\sum_i^{n\_list}c_iq_i=t$. The sum is running over the atoms given in '' |
<code cp2k> | <code cp2k> | ||
& | & | ||
Line 130: | Line 130: | ||
| | ||
\end{equation} | \end{equation} | ||
- | where $t_j$ is the target value for charge $q_j$ and $\beta$ is the strength of the restraint. By default, all elements except hydrogen are weakly restrained to zero, i.e. the keyword [[http:// | + | where $t_j$ is the target value for charge $q_j$ and $\beta$ is the strength of the restraint. By default, all elements except hydrogen are weakly restrained to zero, i.e. the keyword [[inp>FORCE_EVAL/ |
<code cp2k> | <code cp2k> | ||
&RESP | &RESP | ||
Line 148: | Line 148: | ||
</ | </ | ||
In this example, charges on atoms with indexes 1..3 are restrained to -0.18 and the charge on atom 4 to 0.21. The target values $t_j$ of the restraints can be, e.g., inspired from DDAPC, Mulliken charges etc. | In this example, charges on atoms with indexes 1..3 are restrained to -0.18 and the charge on atom 4 to 0.21. The target values $t_j$ of the restraints can be, e.g., inspired from DDAPC, Mulliken charges etc. | ||
- | Note the '' | + | The strength $\beta$ of the restraint is defined by [[inp>FORCE_EVAL/ |
===== Fitting the variance (REPEAT method) ===== | ===== Fitting the variance (REPEAT method) ===== | ||
- | CP2K offers also the possibility to fit the variance of the potential as proposed in * [[ | + | CP2K offers also the possibility to fit the variance of the potential as proposed in [[doi>10.1021/ |
\begin{equation} | \begin{equation} | ||
Line 179: | Line 179: | ||
&END RESP | &END RESP | ||
</ | </ | ||
- | Use the keyword '' | + | Use the keyword '' |
Line 196: | Line 196: | ||
Both errors are printed to the output file. They should be as small as possible. Typical values can be found here:\\ | Both errors are printed to the output file. They should be as small as possible. Typical values can be found here:\\ | ||
- | * [[ | + | |
- | * [[ | + | * [[doi>10.1021/ |
- | * [[ | + | * [[doi>10.1039/ |
When the variance is fitted, $V_{\mathrm{RESP}}$ is shifted by $\delta$ with respect to $V_{\mathrm{QM}}$. Thus, $V_{\mathrm{RESP}}$ is replaced by $\tilde{V}_{\mathrm{RESP}}=V_{\mathrm{RESP}}+\delta$ in the formulas for the RMS and RRMS values.\\ | When the variance is fitted, $V_{\mathrm{RESP}}$ is shifted by $\delta$ with respect to $V_{\mathrm{QM}}$. Thus, $V_{\mathrm{RESP}}$ is replaced by $\tilde{V}_{\mathrm{RESP}}=V_{\mathrm{RESP}}+\delta$ in the formulas for the RMS and RRMS values.\\ | ||
Line 212: | Line 212: | ||
</ | </ | ||
The QM potential can be as well printed as cube file using | The QM potential can be as well printed as cube file using | ||
- | [[https:// | + | [[inp>FORCE_EVAL/ |
===== Example input files ===== | ===== Example input files ===== | ||
* Isolated methanol molecule - nonperiodic fit: {{: | * Isolated methanol molecule - nonperiodic fit: {{: | ||
- | * Metal organic framework IRMOF-1 - periodic fit using REPEAT : {{: | + | * Metal-organic framework IRMOF-1 - periodic fit using REPEAT : {{: |
+ | * Metal-organic framework MIL-53-Al - periodic fit using REPEAT: {{: | ||
+ | * Graphene on Ru(0001) - periodic fit: {{: |
howto/resp.txt · Last modified: 2024/01/15 09:24 by oschuett