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                     GROMACS-4.0.7-ionstr
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This package contains a minor modified version of GROMACS that makes
possible to specify the solution ionic strength as an external
parameter when treating long-range electrostatics with the
Generalized-Reaction-Field (GRF) method [Tironi et al. (1995)
J. Chem. Phys. 102:5451]. The GRF implementation in standard GROMACS
automatically computes the ionic strength from the total charge of the
system, which is an arguable interpretation of the physics behind the
GRF method. The modified version provided here reads the ionic
strength from the variable "ionicstrength" in the .mdp file, similarly
to what is done for other external thermodynamic parameters
(temperature, pressure, etc).

The variable "ionicstrength" corresponds to a number density in units
of nm^-3, which corresponds to 0.6022 units of mol/L (e.g., 0.1 mol/L
= 0.06022 nm^-3). Its default value is zero, in which case GRF becomes
identical to the Reaction-Field method.

This modified GROMACS version was first introduced in the context of
constant-pH MD simulations [Machuqueiro & Baptista (2006)
J. Phys. Chem. B 110:2927], but can be used for standard
(constant-protonation) MD simulations. The modifications provided here
can be easily applied to any GROMACS version.


Authors: Antonio M. Baptista, Miguel Machuqueiro, Sara R. R. Campos

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Modified files:

Modifications for dealing with parameter "ionicstrength" (given in the
.mdp file) were done in the following files:

./include/types/inputrec.h
./include/types/forcerec.h
./src/kernel/readir.c
./src/gmxlib/tpxio.c

Modifications for including the ionic strength (variable "I") in the
function calc_rffac were done in the following files:

./src/mdlib/rf_util.c    (definition of calc_rffac)
./include/force.h        (prototype of calc_rffac)
./src/mdlib/force.c      (calls to calc_rffac)

All modifications can be easily found by searching the string "scampos" in
the corresponding comments.

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