Action: EEFSOLV

Module	colvar
Description	Usage
Calculates EEF1 solvation free energy for a group of atoms.
output value	type
the EEF1 solvation free energy for the input atoms	scalar

Details and examples

Calculates EEF1 solvation free energy for a group of atoms.

EEF1 is a solvent-accessible surface area based model, where the free energy of solvation is computed using a pairwise interaction term for non-hydrogen atoms:

$$\Delta G^\mathrm{solv}_i = \Delta G_i^\mathrm{ref}-\sum _{j \neq i} f _i(r _{ij}) V_j$$

where $\Delta G^\mathrm{solv}_i$ is the free energy of solvation, $\Delta G^\mathrm{ref}_i$ is the reference solvation free energy, $V_j$ is the volume of atom $j$ and

$$f_i(r) 4\pi r^2 = \frac{2}{\sqrt{\pi}} \frac{\Delta G^\mathrm{free}_i}{\lambda_i} \exp\left( - \frac{(r-R_i)^2}{\lambda^2_i}\right)$$

where $\Delta G^\mathrm{free}_i$ is the solvation free energy of the isolated group, $\lambda_i$ is the correlation length equal to the width of the first solvation shell and $R_i$ is the van der Waals radius of atom $i$.

The output from this collective variable, the free energy of solvation, can be used with the BIASVALUE keyword to provide implicit solvation to a system. All parameters are designed to be used with a modified CHARMM36 force field. It takes only non-hydrogen atoms as input, these can be conveniently specified using the GROUP action with the NDX_GROUP parameter. To speed up the calculation, EEFSOLV internally uses a neighbor list with a cutoff dependent on the type of atom (maximum of 1.95 nm). This cutoff can be extended further by using the NL_BUFFER keyword.

Examples

Click on the labels of the actions for more information on what each action computes

#SETTINGS MOLFILE=regtest/basic/rt77/peptide.pdb
MOLINFOThis command is used to provide information on the molecules that are present in your system. More details MOLTYPE what kind of molecule is contained in the pdb file - usually not needed since protein/RNA/DNA are compatible=protein STRUCTUREa file in pdb format containing a reference structure=
regtest/basic/rt77/peptide.pdb
 Click here to see an extract from this file.
  
  ×  
FILE: regtest/basic/rt77/peptide.pdb
    
ATOM      1  N   GLU     1      -0.130   2.450  -0.110  1.00  0.00            
ATOM      2  H1  GLU     1      -0.830   2.960   0.400  1.00  0.00            
ATOM      3  H2  GLU     1       0.640   2.250   0.490  1.00  0.00            
ATOM      4  H3  GLU     1       0.180   3.000  -0.890  1.00  0.00            
ATOM      5  CA  GLU     1      -0.700   1.210  -0.600  1.00  0.00            
...
ATOM    108  HG  SER     9     -26.270  -4.330  14.510  1.00  0.00            
ATOM    109  C   SER     9     -24.110  -4.600  17.630  1.00  0.00            
ATOM    110  O   SER     9     -25.040  -4.470  17.970  1.00  0.00            
ATOM    111  O   SER     9     -23.400  -5.460  18.160  1.00  0.00            
END
  
The MOLINFO action with label  calculates somethingWHOLEMOLECULESThis action is used to rebuild molecules that can become split by the periodic boundary conditions. More details ENTITY0the atoms that make up a molecule that you wish to align=1-111

# This allows us to select only non-hydrogen atoms
#SETTINGS AUXFILE=regtest/basic/rt77/index.ndx
protein-h: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details NDX_FILEthe name of index file (gromacs syntax)=index.ndx NDX_GROUPthe name of the group to be imported (gromacs syntax) - first group found is used by default=Protein-H

# We extend the cutoff by 0.1 nm and update the neighbor list every 40 steps
The GROUP action with label protein-h calculates somethingsolv: EEFSOLVCalculates EEF1 solvation free energy for a group of atoms. More details ATOMSThe atoms to be included in the calculation, e=protein-h

# Here we actually add our calculated energy back to the potential
The EEFSOLV action with label solv calculates the following quantities:
 Quantity   
 Description  
solv.value
the EEF1 solvation free energy for the input atomsbias: BIASVALUETakes the value of one variable and use it as a bias More details ARGthe labels of the scalar/vector arguments whose values will be used as a bias on the system=solv

The BIASVALUE action with label bias calculates the following quantities:
 Quantity   
 Description  
bias.bias
the instantaneous value of the bias potential
bias._bias
one or multiple instances of this quantity can be referenced elsewhere in the input filePRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=solv FILEthe name of the file on which to output these quantities=SOLV

Input

The atoms that serve as the input for this action are specified using one or more of the keywords in the following table.

Keyword	Type	Description
ATOMS	atoms	The atoms to be included in the calculation, e

Full list of keywords

The following table describes the keywords and options that can be used with this action

Keyword	Type	Default	Description
ATOMS	input	none	The atoms to be included in the calculation, e
NL_BUFFERThis keyword do not have examples	compulsory	0.1	The buffer to the intrinsic cutoff used when calculating pairwise interactions
NL_STRIDEThis keyword do not have examples	compulsory	40	The frequency with which the neighbor list is updated
NUMERICAL_DERIVATIVESThis keyword do not have examples	optional	false	calculate the derivatives for these quantities numerically
NOPBCThis keyword do not have examples	optional	false	ignore the periodic boundary conditions when calculating distances
SERIALThis keyword do not have examples	optional	false	Perform the calculation in serial - for debug purpose
TEMP_CORRECTIONThis keyword do not have examples	optional	false	Correct free energy of solvation constants for temperatures different from 298