rdf.inp: main input file

RDF input file consists of several parts: RDF-calculation parameters (&Parameters), definition of Coarse-Grain atom types (&CGTypes), and the list of RDFs to calculate (&RDFsNB, &RDFsB, &RDFsA).

RDF calculation parameters:

(&Parameters ... &EndParameters)
The section describes the input trajectory and defines resolution and cut-off ranges for the reference distribution functions. Note that at this point the trajectory should be already coarse-grained and solvent removed (if the later supposed to be implicit).

The following parameters shall be specified. Old names of the parameters used in MagiC v.1 are stated in parentheses:

OutputFile = <filename>

The name of the output file containing a set of calculated RDFs (FOUTRDF)

TrajFile = <filename>

The name of the CG-trajectory file. (FNAME). The file format will be detected from the extension, or can be stated explicitly in the parameter NFORM

NFORM = <format>

(Optional) Explicitly specified format of the CG-trajectory. Can be XMOL, TRR or XTC. Detected automatically from the trajectory file extension.

BeginFile=<value>, EndFile=<value>

(Optional) If the trajectory is split into a number of files emumetated by file name extentions (.001, .002, .003, ...), these parameters specify a range of the files to read. (NFBEG, NFEND)

Step = <value>

(Optional) How often to read frames from the trajectory (ISTEP). Default: 1 (read every frame)

NMType = <value>

Number of molecular types present in the CG-trajectory. (NTYPES)

NameMType = Type1, Type2, ... , Type(NMType)

Names of molecular types present in the system. Each type should have a molecular description file, having the same name as the molecular type (NAMOL)

NMolMType = Num1, Num2, ... ,Num(NMType)

Number of molecules of each molecular type present in the system (NSPEC)

RMaxNB=<value>

Cut-off distance for intermolecular / non-bonded RDFs (RDFCUT)

RMaxB=<value>

Cut-off distance for intramolecular RDFs (RMAX)

ResolNB=<value>

Resolution (Å) of the histogram for intermolecular RDF calculation (DELTAR)

ResolB=<value>

Resolution (Å) of the histogram for intramolecular RDF calculation (DELTARI)

ResolA=<value>

Resolution (degrees) of the histogram for intramolecular angular distrubution functions calculation (DELTAPHI)

Box= <X> <Y> <Z>

Size of the periodic box (Å) used as PBC. Optional. Used only if the periodic cell size was not specified in the trajectory file.

Bead types:

(&CGTypes, ... , &EndCGTypes)
Here bead types (CG-atom types) are introduced and beads belonging to each type are specified. This is done by a list of lines having a format
<Name of CG-type>:<NameBead1 NameBead2 NameBead3>, one line per each type, bead names are space separated. Note, that the order of bead type lines will define indexes of the bead types set in the .mcm -files.

Non-Bonded RDFs

(&RDFsNB, ... , &EndRDFsNB)
Here we define a list of reference distribution functions for non-bonded interactions, which are radial distribution functions. For each function a list of bead-pairs (CG atom pairs) involved in the specific interaction shall be provided. It is possible to generate the list automatically between all or some of pairs of bead types using the following commands:

add: all
This will generate automatically a list of RDFs which includes all possible RDFs based on pair combinations of CG-atom types. For each pair of CG-atom types a RDF will be determined, which includes all pairs of CG atoms of the specified types, and effective potential for this pair of atom types will be calculated on the next stage. With this option, all possible NB-RDFs will be taken into account. This is the most common regime.

add: <CGType> -- <CGType>
Create a list of CG-atom pairs having the given CG-atom types, and include it into calculation of RDFs. This will add a single RDF to the list.

add: <CGType1> -- <CGType2>: AName1 AName2, AName3 AName4
Explicitly add pairs of atoms AName1-AName2, AName3-AName4 to the RDF for the given pair of CG-atom types. This is the most specific way of setting the atom-pairs list for a given RDF.

del: <CGType> -- <CGType>
Remove a specific RDF (interaction) from the set of RDFs generated up to this line.

del: <CGType> -- <CGType>: AName1 AName2, AName3 AName4
Exclude a specific pair of atoms from the RDF for given atom types.

RDFs for Pairwise Bonds

(&RDFsB, ... , &EndRDFsB)

In this section reference distributions for pairwise bonds (e.g. bond length distributions) will be specified. Note that this is important information which determines bonding in the CG molecule, which has to be specified explicitly.

Each bond should be specified by the following line: For every independent bond type the molecular type it belongs to should be specified, with the relative index of the bond and atom pairs involved in the bond.

add: <MolType>: <BondIndex>: <AName1> <AName2>, <AName3> <AName4>
where <MolType> is index of the molecular type, <BondIndex> is the index of the bond in the given molecular type, and pairs <AName1> <AName2>, <AName3> <AName4>,... determine CG atoms within the molecule connected by the given bond type.

RDFs for Angle-bending bonds

(&RDFsA, ... , &EndRDFsA)
In this section reference distributions for angle-bending bonds (e.g. bond angle distribution) are determined. It can be done manually, similar to specifying pairwise bonds, or deduced automatically by setting an A-bond between every two interconnected pairwise bonds (excluding cases when the end atoms of the angle are already connected by a bond). Note that pairwise bonds shall be set in prior, i.e &RDFsA-section shall go after &RDFsB-section. The following keywords can be used in this section:

add: all
Automatically deduce angle-bending bonds for all molecular types of the system

add: MolType : all
Automatically deduce angle-bending bonds in the given molecular type

add: <MolType>: <BondIndex>: <AName1> <AName2> <AName3>, ..., ...
Explicitly add triplet (triplets) of atoms to the given angle-bending bond of the given molecular type

del: MolType : all
Discard all angle-bending bonds in the given molecular type

del: MolType : <BondIndex>
Discard given A-bond

del: MolType : <BondIndex>: <AName1> <AName2> <AName3>, ...,
Remove given atoms from the defined previously A-bond

Note that every pair of atom involved in a bond (pairwise or angle-bending) is automatically excluded from non-bonded RDF calculation and from non-bonded interactions.