![]() ![]() In this case, all atoms within the sphere at the start of the calculation are active throughout the calculation, while all other atoms are inactive. If four real number modifiers are provided, the first three are taken as X-, Y- and Z-coordinates and the fourth is the radius of a sphere centered at these coordinates. Provides an alternative to the ACTIVE and INACTIVE keywords for specification of subsets of active atoms. The presence of any ACTIVE keyword overrides any INACTIVE keywords in the keyfile. On each line the keyword can be followed by one or more atom numbers or atom ranges. Multiple ACTIVE lines can be present in the keyfile and are treated cumulatively. For torsional space calculations, rotations are allowed when all atoms on one side of the rotated bond are active. For Cartesian space calculations, active atoms are those allowed to move. Individual potential energy terms are computed when at least one atom involved in the term is active. Sets the list of active atoms during a Tinker computation. Sets the value of the “A” premultiplier term in the Buckingham van der Waals function, i.e., the value of A in the formula Evdw = epsilon *. The length value in Angstroms is provided following the keyword. Sets the value of the a-axis length for a crystal unit cell, or, equivalently, the X-axis length for a periodic box. The format of possible modifiers, if any, is shown in brackets following each keyword. The following is an alphabetical list of the Tinker keywords along with a brief description of the action of each keyword and required or optional parameters that can be used to extend or modify each keyword. For example, the keyword line ACTIVE 4 -9 17 23 could be used to add atoms 4, 9 through 17, and 23 to the set of active atoms during a Tinker calculation. If a range of numbers is desired, it can be specified by listing the negative of the first number of the range, followed by a separator and the last number of the range. For these keywords the integers can simply be listed explicitly and separated by spaces, commas or tabs. Several keywords take a list of integer values (atom numbers, for example) as modifiers. Any lines contained in the keyfile which do not qualify as valid keyword lines are treated as comments and are ignored. ![]() Modifier information is read in free format, but must be completely contained on the same line as the original keyword. Some keywords take modifiers i.e., Tinker looks further on the same line for additional information, such as the value of some parameter related to the keyword. Any blank space to the left of the keyword is ignored, and all contents of the keyfiles are case insensitive. All keywords must appear as the first word on the line. Tinker searches the keyfile during the course of a calculation for relevant keywords that may be present. If a keyfile is not located via any of the above mechanisms, Tinker will continue by using default values for keyword options and asking interactive questions as necessary. Will run the Tinker ANALYZE program taking as input the molecular system given in the file “my-molecule” or “my-molecule.xyz”, and using a keyfile named either “my-keyfile” or “my-keyfile.key”. ![]()
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