rdf.inp: main input file

RDF input file consists of several parts: RDF-calculation parameters (&Parameters), definition of Coarse-Grain atom types (&CGTypes), the list of RDFs to calculate (&RDFsNB, &RDFsB, &RDFsA) and optional declaration (&SameAsBond) that some bonds in different molecules are equivalent, which means that their distributions are averaged, and they are assigned the same bonded potential in the CG model. The later is a formal way to have the same type of bond in several different molecular types.

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 reference all-atom trajectory should be already mapped into coarse-grained representation.

The following parameters shall be specified:

*OutputFile = <filename>: The name of the output file containing a set of calculated RDFs
*TrajFile = <filename>: The name of the CG-trajectory file. 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.
Step = <value>: (Optional) How often to read frames from the trajectory. Default: 1 (read every frame)
BeginFile=<value>, EndFile=<value>: (Optional) If the trajectory is split into a number of files enumerated by file name extensions (.001, .002, .003, ...), these parameters specify a range of the files to read.
*NMType = <value>: Number of molecular types present in the CG-trajectory.
*NameMType = Type1, Type2, ... , Type(NMType): Names of the molecular types. Each type should have a molecular description file (.CG.mmol), having the same name as the molecular type.
*NMolMType = Num1, Num2, ... ,Num(NMType): Number of molecules of each molecular type present in the system.
*RMaxNB=<value>: Cut-off distance (Å) for intermolecular / non-bonded RDFs
*RMaxB=<value>: Cut-off distance (Å) for intramolecular bond length distributions
*ResolNB=<value>: Resolution (Å) of the histogram for intermolecular RDF calculation
NAngleBondsExclude=<value1>,...,<valueNMType>
NPairBondsExclude=<value1>,...,<valueNMType>: Atoms having this many pairwise/angle-bending bonds between, will be excluded from non-bonded distributions. User can specify individual value for each molecular type or one value for all of them. Special case: -1 exclude all intramolecular pairs. Default value: 1 (corresponds to exclusion of all intramolecular pairs involved in one of bonded or bending angle interactions).

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 in the .mcm-files.

Non-Bonded RDFs

(&RDFsNB, ... , &EndRDFsNB)
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 precise 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) are specified. Note that this determines bonding in the CG molecule, and thus has to be specified explicitly.

For each independent pairwise bond type one need to specify the molecular type it belongs to, the relative index of the bond, and list of atom pairs connected by the bonds of this type. This is done in a single line record:
add: <MolType>: <BondIndex>: <AName1> <AName2>, <AName3> <AName4>
where <MolType> the molecular type, <BondIndex> the bond type index in the given molecular type, and pairs <AName1> <AName2>, <AName3> <AName4>,... determine CG atoms within the molecule connected by bonds of the <BondIndex> 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, similarly 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 appear 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 the given A-bond

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

Same Type of the Bond declarations:

(&SameAsBond ... &EndSameAsBond)
This section has recently appeared in MagiC as a formal way to describe bonds belonging to different molecular types by the same RDF/potential. The MagicCore was written in assumption that different molecular types must have different bonds. To overcome this limitation, we made possibility to link a "secondary" bond to another "original" bond. In all resulting files this two bonds will appear separately, however they will have same distributions. The linking - records have format:
OriginalBond = LikedBond1, LinkedBond2,....
Each bond is specified as MolecularTypeName:BondNumber, see example below.

 &SameAsBond
 DMPC.CG:1 = DMPC.CG:3, DMPC.CG:4
 DMPC.CG:2 = DMPC2.CG:1 
 &EndSameAsBond