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HOWTO
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HOWTO
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REFERENCES
========================================================
For the GITIM algorithm, and for the Monte Carlo normalization
procedure:
REF1 M. Sega, S. S. Kantorovich, P. Jedlovszky and M. Jorge,
"The generalized identification of truly interfacial
molecules (ITIM) algorithm for nonplanar interfaces",
accepted for publication on J. Chem. Phys., vol. 138.
Alternatively, http://arxiv.org/abs/1210.2981
For the ITIM algorithm,
REF2 L. B. Pártay, G. Hantal, P. Jedlovszky, A. Vincze, and
G. Horvai,
J. Comput. Chem. 29, 945 (2008).
CONTACT
========================================================
EMAIL: You can contact me at [email protected]
please let me know if you found the software useful,
if you found bugs or if you have feature requests.
COMPILING
========================================================
create a build directory, e.g. inside the source tree:
cd g_density/
mkdir build
cd build
launch cmake providing the location of your gromacs tree
and your gromacs build, e.g.
cmake .. -DMYGMX_TREE=~/gromacs-5.0.6/ -DMYGMX_BUILD=~/gromacs-5.0.6/build/
compile
make
KNOWN BUGS
========================================================
* -dump assumes that -ng 3 is used, and segfaults when less than
three groups are supplied.
* -dump in conjunction with -com fails in dumping the correct
surface atoms.
* -center should be switched on automatically with -intrinsic
UNKNOWN BUGS
========================================================
Possibly many. Not all combinations of different options have
been tested, and some might result in unpredictable behavior.
USAGE DESCRIPTION
========================================================
To enable the ITIM analysis, the option -intrinsic should be turned
on. The mass and number intrinsic density profiles can then be
calculated with the -dens option. At least two and at most three
groups should be supplied with the option -ng, the first of which
(the "support" group) is used to define the surface, while the
remaining ones are used to compute the intrinsic density profiles.
The option -center uses an heuristic algorithm to center the atoms
of the support group in the simulation box. The option -dump saves
the surface atoms and those of the other groups in a .gro file
(multiple frames will be appended to the same file) named surf.gro,
phase.gro and phase2.gro, respectively. The option -com is used
to compute the density profiles using the molecular center of mass
of molecules or residues, instead of the of the atomic density
profiles. A file named masscom.dat should be present, listing the
number of atoms in the molecule/residue for each group, space-separated.
A zero has to be used when no center of mass calculation should be
used.
USAGE EXAMPLES
========================================================
In the example/ directory the basic files for running a simulation
of a CCl4/water mixture are provided. The script RUN.sh runs some
minimal tests using one configuration instead of a trajectory. The
.tpr which is generated can anyway be used to produce a full
trajectory if needed.
To perform the ITIM analysis one needs:
* a configuration or a trajectory
* the relative .tpr file
* a file named masscom.dat (for the -com option only) containing
the number of atoms in each molecule
A typical command line to analyze the intrinsic density profile in
a two component liquid looks like:
g_density -intrinsic -dens mass -f traj.trr -s topol.tpr -ng 3 -center -sl 200 -o density.xvg -MCnorm
where three groups are supplied: the first one is used to construct
the interface, and the other two are the two groups of which the
intrinsic density profile will be computed.
The output file will contain 4 columns, the location of the bin,
the distribution of surface atoms, and the intrinsic density profiles
of the atoms in the last two groups.
The option -MCnorm switches on the Monte Carlo normalization (see
Sec IV in REF 1), that provides an improved calculation of the
intrinsic density profiles, removing the smearing caused by the
periodic copy of the fluctuating interface
If the configurations of the surface atoms are needed, for visualization
or for further analysis, they can be saved to disk using the -dump
option, which creates the files surf.gro, phase.gro and phase2.gro.
The first file contains the configurations of the surface atoms,
while the last two contain the configurations of the atoms in the
last two groups (they differ from those that can be extracted from
the trajectory as they are shifted)
If one wants to analyze the molecular density profiles, rather than
the atomic ones, it is possible to use the option -com. In this
case, one needs to supply also a file named masscom.dat, that
contains on one line the number of atoms composing the molecules
in each group, using a value of 0 when no molecular center of mass
calculation has to be performed (e.g., for the first group).