Force GROMOS

In this case, only two parameters (k and Iq) per atom pair are needed, and the computation of a quadratic function is less expensive. Therefore, this type of expression is used especially by biomolecular force fields (AMBER, CHARMM, GROMOS) dealing with large molecules like proteins, lipids, or DNA. 

Gronigen molecular simulation (GROMOS) is the name of both a force field and the program incorporating that force field. The GROMOS force field is popular for predicting the dynamical motion of molecules and bulk liquids. It is... 

In order for this to work, the force field must be designed to describe inter-molecular forces and vibrations away from equilibrium. If the purpose of the simulation is to search conformation space, a force field designed for geometry optimization is often used. For simulating bulk systems, it is more common to use a force field that has been designed for this purpose, such as the GROMOS or OPLS force fields. 

Oostenbrink, C. Villa, A. Mark, A. E van Gunsteren, W. F., A biomolecular force field based on the free enthalpy of hydration and solvation the Gromos force-field parameter sets 53A5 and 53A6., J. Comput. Chem. Oct 2004, 25, 1656-1676. 

Tab. 1.3 Comparison between different sets of atomic point charges for a zwitterionic Gly-Ala dipeptide in aqueous solution. D-RESP electrostatic potential derived charges [12] fitted to all 36 configurations. Hirshfeld average value of the Hirshfeld charges [89c] along the full trajectory, Amber AMBER 1995 force field [86], Gromos GROMOS96 force field [85], The charges of equivalent atoms are imposed to be equal.

MD simulations provide a detailed insight in the behavior of molecular systems in both space and time, with ranges of up to nanometers and nanoseconds attainable for a system of the size of a CYP enzyme in solution. However, MD simulations are based on empirical molecular mechanics (MM) force field descriptions of interactions in the system, and therefore depend directly on the quality of the force field parameters (92). Commonly used MD programs for CYPs are AMBER (93), CHARMM (94), GROMOS (95), and GROMACS (96), and results seem to be comparable between methods (also listed in Table 2). For validation, direct comparisons between measured parameters and parameters calculated from MD simulations are possible, e.g., for fluorescence (97) and NMR (cross-relaxation) (98,99). In many applications where previously only energy minimization would be applied, it is now common to perform one or several MD simulations, as Ludemann et al. and Winn et al. (100-102) performed in studies of substrate entrance and product exit. 

Allen and Bevan (80) have applied the SMD technique to the study of reversible inhibitors of monoamine oxidase B, and this paper will be used as an example for discussion of the constant velocity SMD pulling method. They used the Gromacs suite of biomolecular simulation programs (18) with the united-atom Gromos 43al force field to parameterize the lipid bilayer, protein, and small-molecule inhibitors. The protein was inserted into their mixed bilayer composed of phosphatidyl choline (POPC) and phosphatidyl ethanolamine (POPE) lipids in a ratio known to be consistent for a mitochondrial membrane. Each inhibitor-bound system studied was preequilibrated in a periodic box of SPC water (20) with the simulations run using the NPT ensemble at 300 K and 1 atm pressure for 20 ns. Full atomic coordinates and velocities were saved in 200-ps increments giving five replicates for each inhibitor-bound system. A dummy atom was attached to an atom (the SMD atom shown in Fig. 7) of the inhibitor nearest to the... 

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