g_mmpbsa

MM/PBSA method for GROMACS.

This project is maintained by RashmiKumari

Input Keywords for Non-polar Solvation Energy

apolar
apolar            = yes

This will specify whether to do non-polar calculation. Value yes will allow the calculation wheras value no will not allow the calculation.

SASA model

gamma
gamma            =  0.02267

This specifies the surface tension proportionality term (kJ mol -1 Å -2 ) of the solvent. With gamma = 0, SASA energy is not calculated.


sasaconst
sasaconst        = 3.84928

Offset or constant c in (kJ mol-1) from E = γ * SASA + c


sasrad
sasrad           = 1.4

Solvent probe radius in Å to calculate solvent accessible surface area.


SAV model


press
press            = 0.234304

This specifies the solvent pressure proportionality term (kJ mol-1 Å-3). With press = 0, SAV energy is not calculated.


savrad
savrad           = 1.29

Solvent probe radius in Å to calculate solvent accessible volume.


savconst
savconst         = 0

Offset or constant c in kJ/mol from E = ( p * SAV ) + c


Continuum/Integral based model (WCA-like)

WCA
WCA              = yes

Switch for WCA method: “yes” or “no”


wcarad
wcarad           = 1.25

Solvent probe radius for WCA method. This specify the radius of solvent molecules and used to define various solvent-related surfaces and volumes. This keyword is ignored when srfm is spl2. For more details, see apolar keyword srad here


bconc
bconc            =  0.033428

This parameter specifies the bulk solvent density in Å-3. This can set to zero to eliminate integral contributions to nonpolar solvation energy calculation. For more details, see apolar keyword bconc here.


dpos
dpos             = 0.05

This specify the displacement in Å of the atomic positions for surface area derivative calculation using finite difference method. For more details, see apolar keyword dpos here.


grid
grid             = 0.4 0.4 0.4

This parameter specifies the quadrature grid spacing in Å for volume integral calculations. For more details, see apolar keyword grid here.


APsdens
APsdens          = 200

This specifies the number of quadrature points per Å2 to use for molecular surface or solvent accessible surface. The parameter is ignored when the srad = 0.0 or when srfm = spl2. For more details, see apolar keyword sdens here.


APsrfm
APsrfm           = sacc

This parameter specifies the model used to construct the solvent-related surface and volume. For more details, see apolar keyword srfm here.


APswin
APswin           = 0.3

This specify the size of spline window in Å for spline-based surface definitions.For more details, see apolar keyword swin here.


APtemp
APtemp           = 300 

This parameter specifies the temperature for apolar calculation. For more details, see apolar keyword temp here.