The HQBM Module of CHARMM By Emanuele Paci, 1997/2000 HQBM is an external perturbation designed induce conformational changes in macromolecules. The time dependent perturbation is designed to introduce a very small perturbation to the short time dynamics of the system and does not affect the conservation of the constants of motion of the system (the conservation of the total energy or of the suitable conserved quantity when an extended Lagrangian is used can then be used as a check of the correctness of the forces). The external perturbation needs: - a reference (or target) structure - a reaction coordinate which defines a "distance" from the reference structure * Menu: * Syntax:: Syntax of the HQBM command * Function:: Purpose of each of the keywords * Input:: HQBM Input Description

[INPUT HQBM command] - read the reference structure OPEN UNIT 1 READ FORMATTED NAME coor0.crd READ COOR CARD COMP UNIT 1 CLOSE UNIT 1 - call the perturbation choosing a coupling constant [ALPHA], a reaction coordinate [RC1, RC2 or RC3], and a selection of atoms which define the reaction coordinate. HQBM [AWAY] ALPHA real [RC1] atom-selection [READLIST integer] [IUNJ integer] [EVAL real] [TARGet real] - energy has to be called immediately after HQBM !! ENERGY

The following section describes the keywords of the HQBM command. HQBM introduces a half quadratic perturbation on a given reaction coordinate (see below) Meaning of the HQBM parameters 1) AWAY drive the system away from the reference structure. As an example, if the reaction coordinate measures the deviation from a reference conformation, the perturbation will increase it. 2) ALPHA is the force constant of the half harmonic potential. 3) RC1, RC2, RC3 will select other reaction coordinates (which can be user-redefined) 4) atom-selection: only the atom selected, for both the actual and reference structure, enter in the above defined reaction coordinate. Example: if the reference structure has all the coordinates equal to zero, and only two atoms are selected, the reaction coordinate is equal to the square of the distance between the two atoms. 5) In alternative to a atom-selection a file can be read from unit READLIST which looks like this one n i1 j1 ..... in jn In this case the reaction coordinate is given by the sum of n terms (r_{ij}(t)-r_{ij}^R)^2 where ij are the pairs given in the list 6) IUNJ: write the output (istep rc(t) max(rc)) on unit IUNJ 7) EVAL: specify the exponent for the RC1 formula. Note that if value 2 is specified with EVAL keyword square root of the original RC1 formula is used. If you dont specify EVAL keyword the original is used. When EVAL is specified the general formula is: \rho(t)=(\frac{1}{N(N-1)}\sum_{i=1}^N\sum_{j\ne i}^N (r_{ij}(t)-r_{ij}^R)^{eval})^\frac{1}{eval} 8) TARGet: one can specify the target value for the \rho (default = 0) As an example, RC1 corresponds to \rho(t)=\frac{1}{N(N-1)}\sum_{i=1}^N\sum_{j\ne i}^N(r_{ij}(t)-r_{ij}^R)^2 where r_{ij}=r_i-r_j and r_i^R are the coordinates of the reference structure. If the reference structure has all the coordinates zero, the reaction coordinate will be the radius of gyration. If the reference structure is the experimental structure the reaction coordinate will be a measure of the instantaneous "distance" from that, analogous to mean square deviation. The method is described in E. Paci and M. Karplus. Forced unfolding of fibronectin type 3 modules: An analysis by biased molecular dynamics simulations. J. Mol. Biol., 288: 441-459, 1999.

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