EEFSOLV

This is part of the colvar module

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:

\[ \Delta G^\mathrm{solv}_i = \Delta G^\mathrm{ref}_i - \sum_{j \neq i} f_i(r_{ij}) V_j \]

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
MOLINFO 
MOLTYPE
compulsory keyword ( default=protein )
what kind of molecule is contained in the pdb file - usually not needed since protein/RNA/DNA
are compatible 
=protein 
STRUCTURE
compulsory keyword 
a file in pdb format containing a reference structure. 
=peptide.pdb The MOLINFO action with label 
WHOLEMOLECULES 
ENTITY0
the atoms that make up a molecule that you wish to align. 
=1-111 The WHOLEMOLECULES action with label 
# This allows us to select only non-hydrogen atoms
#SETTINGS AUXFILE=regtest/basic/rt77/index.ndx
protein-h: GROUP 
NDX_FILE
the name of index file (gromacs syntax) 
=index.ndx 
NDX_GROUP
the name of the group to be imported (gromacs syntax) - first group found is used
by default 
=Protein-H The GROUP action with label protein-h defines a group of atoms so that they can be referred to later in the input
# We extend the cutoff by 0.1 nm and update the neighbor list every 40 steps
solv: EEFSOLV 
ATOMS
The atoms to be included in the calculation, e.g. 
=protein-h The EEFSOLV action with label solv calculates a single scalar value
# Here we actually add our calculated energy back to the potential
bias: BIASVALUE 
ARG
the input for this action is the scalar output from one or more other actions. 
=solv The BIASVALUE action with label bias calculates the following quantities:

 Quantity   
 Description  
bias.bias
the instantaneous value of the bias potential
bias.solv_bias
one or multiple instances of this quantity can be referenced elsewhere in the input file. these quantities will named with  the arguments of the bias followed by the character string _bias. These quantities tell the user how much the bias is due to each of the colvars. This particular component measures this quantity for the input CV named solv


PRINT 
ARG
the input for this action is the scalar output from one or more other actions. 
=solv 
FILE
the name of the file on which to output these quantities 
=SOLV The PRINT action with label 

Glossary of keywords and components

The atoms involved can be specified using

ATOMS

The atoms to be included in the calculation, e.g. the whole protein.. For more information on how to specify lists of atoms see Groups and Virtual Atoms

Compulsory keywords

NL_BUFFER	( default=0.1 ) The buffer to the intrinsic cutoff used when calculating pairwise interactions.
NL_STRIDE	( default=40 ) The frequency with which the neighbor list is updated.

Options

NUMERICAL_DERIVATIVES	( default=off ) calculate the derivatives for these quantities numerically
NOPBC	( default=off ) ignore the periodic boundary conditions when calculating distances
SERIAL	( default=off ) Perform the calculation in serial - for debug purpose
TEMP_CORRECTION	( default=off ) Correct free energy of solvation constants for temperatures different from 298.15 K