Syntax

SHAKe

{ $<$shake-statement$>$ } END is invoked from the main level of X-PLOR.

$<$shake-statement$>$:==

ANGLe $<$selection$>$ $<$selection$>$ $<$selection$>$

adds new SHAKE constraints to the SHAKE database. The program goes through the list of bond angles of the molecular structure, trying to match them against the triple atom selection. If the first and third atoms of the angle match the first and the third selections or vice versa, and if the second atom matches the second selection, a SHAKE constraint of the distance between the first and third atoms is added to the database. For parameter-based SHAKE angle constraints (REFErence=PARAmeter), type-based parameters will be retrieved for both the bond angle and the bond lengths. Thus, the type-based parameter database needs to contain the corresponding bond and bond angle parameters. The atom-based parameter database has no influence on this statement (default: none).

BOND $<$selection$>$ $<$selection$>$

adds new SHAKE constraints to the SHAKE database. The program goes through the list of covalent bonds of the molecular structure, trying to match them against the double atom selection. If one atom of the bond matches the first selection and the other atom matches the second selection, a SHAKE constraint of this bond distance is added to the database. For parameter-based SHAKE bond constraints (REFErence=PARAmeter), the atom- and type-based parameter databases are consulted in order to retrieve the required bond length (default: none).

MOLEcule $<$selection$>$

adds new SHAKE constraints to the SHAKE database. The program goes through all interatom distances of the selected atoms that belong to the same nonbonded group (see Section 3.1.1) and adds to the database a SHAKE constraint of the interatom distance. Normally, this statement is used to SHAKE small molecules such as waters.

MXITerations=$<$integer$>$

specifies the maximum number of SHAKE iterations that are allowed before the SHAKE procedure exits with an error condition (default: 500).

NCONstraints=$<$integer$>$

is a parameter that allocates space for SHAKE constraints. The specified $<$integer$>$ should be greater than or equal to the actual number of SHAKE constraints (default: 4000).

REFErence=

COORdinates $\vert$ PARAmeters determines whether the reference distances for the SHAKE constraints will come from the main coordinate set or from the parameters. This statement has to be specified before the MOLEcule, BOND, or ANGLe statements (default: COORdinate).

RESEt

erases the current SHAKE database.

TOLErance=$<$real$>$

specifies the point at which the SHAKE iterations are terminated (default: 1.0e-05). The tolerance is satisfied if the deviation of the constrained distances is less than the tolerance times the actual distance.