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| 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.
| 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 |
| 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. |
| 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 |
#SETTINGS MOLFILE=regtest/basic/rt32/helix.pdb MOLINFO MOLTYPE=protein STRUCTURE=peptide.pdb WHOLEMOLECULES ENTITY0=1-111 # This allows us to select only non-hydrogen atoms protein-h: GROUP NDX_FILE=index.ndx NDX_GROUP=Protein-H # We extend the cutoff by 0.1 nm and update the neighbor list every 40 steps solv: EEFSOLV ATOMS=protein-h NL_STRIDE=40 NL_BUFFER=0.1 # Here we actually add our calculated energy back to the potential bias: BIASVALUE ARG=solv PRINT ARG=solv FILE=SOLV
1.8.14