cgtraj.inp: main input file

The file consists of two parts. The first part describes the input atomistic trajectory, and the second one describes CG-bead mapping scheme.

Trajectory reading subroutine was inherited from tranal utility of MDynaMix, and it has the same syntax. The first part of the input file is written in Fortran NAMELIST format which looks like:

 $TRAJ
 parameter=value(s),
 ...
 $END

“TRAJ” is the name of this NAMELIST section. The following parameters shall be defined (* denotes mandatory parameters):

*FNAME = <file_name> Name of the trajectory file or a base name of the set of files¹. The trajectory (except XTC) can be written as a sequence of files <file_name>.001 , <file_name>.002 and so on, the largest possible number being <file_name>.9999.

*NFORM = <format>
where <format> is one of:

XTC - XTC compressed binary trajectory format (GROMACS, LAMMPS)
TRR - TRR binary trajectory format (GROMACS)
XMOL - XMOL trajectory. It is assumed, that the commentary (second) line of each configuration is written in the format:
(char) <time> (char-s) BOX: <box_x> <box_y> <box_z> where (char) is any character word, <time> is time in , <box_x> <box_y> <box_z> (following after keyword BOX) are the box sizes in A.
PDBT - PDB trajectory as generated by “trjconv” utility of GROMACS simulation package.
DCDT - DCD trajectories generated by NAMD package

*NTYPES = <value>
Number of molecule types in the trajectory

*NAMOL = <name1>, <name2>, ... <name_NTYPES>
List of molecular type names. It is recommended that files <name1>.mmol, <name2>.mmol,... describing the molecules are present in the directory defined by PATHDB. Format of .mmol files is the same as for MDynaMix program. For analyzing trajectories generated by other programs, .mmol files are still used to provide information about atomic masses and charges. It is however enough to have only the first section of .mmol files containing description of atoms.

The program may work without .mmol files, if parameters NSPEC and NSITS (see below) are given. In this case, the masses of all atoms are set to 1 and the charges to 0, which will result in definition of CG sites as geometric centers of the atomic groups, and zero charges of CG sites (the later can be manually corrected at the next stage).

*NSPEC = <n1>, <n2>, ..., <n_NTYPES>
Number of molecules of each type ( NTYPES numbers in total).

NSITS = <n1>, <n2>, ..., <n_NTYPES>
Number of atoms in each molecular type ( NTYPES numbers in total). This parameter is not necessary if .mmol files for each molecular type are provided.

PATHDB = <value>
Directory with molecular description files (.mmol). Default is the current directory (.)

NFBEG = <value>
Number of the first trajectory file (integer between 0 and 9999)

NFEND = <value>
Number of the last trajectory file (integer between 0 and 9999)

IPRINT = <value>
Defines how much you see in the intermediate output. The final output with analysis of results does not depend on it. Default value is 5.

BOXL = <x-box-size>

BOYL = <y-box-size>

BOZL = <z-box-size>

define the box size (in A) if it is not present in the trajectory (can be used in case of constant-volume simulation) If information of the box sizes is present in the trajectory, box size parameters from the input file are ignored.

ISTEP = <value>
Specifies that only each ISTEP-th configuration from the trajectory is taken for the analysis. Default is 1.

The second part of the file describes CG bead mapping scheme. The whole section starts with keyword: BeadMapping and ends with EndBeadMapping. Every coarse grain molecular type has to be described in a separate subsection, which starts with tag CGMolecularType: <CGMolecularTypeName> and ends with EndCGMolecularType. Inside such a section, the parental molecular type name and CG beads definition should be given. The parent's name is defined by the tag ParentType: <ParentMolecularTypeName>
CG beads are defined in a one-line-per-bead way, where every line has the following structure:
<Bead name>:<N of atoms in the bead>:<list of atoms atom1,atom2,...>, where list of atoms is a comma separated list of atom numbers according to the mmol-file describing parental molecular type. User can also put intervals instead of a single number, e.g. 1-3,5,7-9,10 instead of 1,2,3,5,7,8,9,10. NB! The keywords/tags are not case sensitive, and spaces will be automatically removed from the text.

Once cgtraj is executed, it generates a bead-mapped trajectory (in case of xtc-format, user also gets the last frame saved in last_frame.xmol, which is handy for VMD-visualization). Also file named <CGMolecularTypeName>.CG.mmol will be created for every defined CG-molecular type.