Prm File

Prm File Format
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Non-bonded parameters¶

The PRM file type is primarily associated with BullsEye Style File. How can I open a PRM file? You need a suitable software like BullsEye Style File to open a PRM file. Without proper software you will receive a Windows message 'How do you want to open this file?' (Windows 10) or 'Windows cannot open this file' (Windows 7) or a similar Mac. A mesh is a group of polies. While.w file contains many meshes,.prm file contains only one mesh (group of polies). A polygon in a computer graphics (image generation) system is a two-dimensional shape that is modelled and stored within its database. A polygon can be colored, shaded and textured, and its position in the database is defined by the coordinates of its vertices (corners).

The non-bonded parameters consist of the van der Waals parameters V (c6or (sigma), depending on the combination rule) and W (c12 or(epsilon)), as listed in the file ffnonbonded.itp, where ptype isthe particle type (see Table 10). As with the bondedparameters, entries in [*type] directives are applied to their counterparts inthe topology file. Missing parameters generate warnings, except as notedbelow in section Intramolecular pair interactions.

Note that most of the included force fields also include the at.num.column, but this same information is implied in the OPLS-AA bond_typecolumn. The interpretation of the parameters V and W depends on thecombination rule that was chosen in the [defaults] section of the topology file(see Topology file):

(1)¶[begin{split}begin{aligned}mbox{for combination rule 1}: & &begin{array}{llllll} mbox{V}_{ii} & = & C^{(6)}_{i} & = & 4,epsilon_isigma_i^{6} & mbox{[ kJ mol$^{-1}$ nm$^{6}$ ]} mbox{W}_{ii} & = & C^{(12)}_{i} & = & 4,epsilon_isigma_i^{12} & mbox{[ kJ mol$^{-1}$ nm$^{12}$ ]}end{array}mbox{for combination rules 2 and 3}: & &begin{array}{llll} mbox{V}_{ii} & = & sigma_i & mbox{[ nm ]} mbox{W}_{ii} & = & epsilon_i & mbox{[ kJ mol$^{-1}$ ]}end{array}end{aligned}end{split}]

Some or all combinations for different atom types can be given in the[nonbond_params] section, again with parameters V andW as defined above. Any combination that is not given will be computedfrom the parameters for the corresponding atom types, according to thecombination rule:

(2)¶[begin{split}begin{aligned}mbox{for combination rules 1 and 3}: & &begin{array}{lll} C^{(6)}_{ij} & = & left(C^{(6)}_i,C^{(6)}_jright)^{frac{1}{2}} C^{(12)}_{ij} & = & left(C^{(12)}_i,C^{(12)}_jright)^{frac{1}{2}}end{array}mbox{for combination rule 2}: & &begin{array}{lll} sigma_{ij} & = & frac{1}{2}(sigma_i+sigma_j) epsilon_{ij} & = & sqrt{epsilon_i,epsilon_j}end{array}end{aligned}end{split}]

When (sigma) and (epsilon) need to be supplied (rules 2and 3), it would seem it is impossible to have a non-zero (C^{12})combined with a zero (C^6) parameter. However, providing anegative (sigma) will do exactly that, such that (C^6) isset to zero and (C^{12}) is calculated normally. This situationrepresents a special case in reading the value of (sigma), andnothing more.

Prm File Format

There is only one set of combination rules for Buckingham potentials:

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(3)¶[begin{split}begin{array}{rcl}A_{ij} &=& left(A_{ii} , A_{jj}right)^{1/2} B_{ij} &=& 2 / left(frac{1}{B_{ii}} + frac{1}{B_{jj}}right) C_{ij} &=& left(C_{ii} , C_{jj}right)^{1/2}end{array}end{split}]