GROMOS program

Cyclodextrins have had valuable industrial uses for a considerable time, particularly as agents to bind or release volatile molecules. Accurate predictions concerning the selectivity and stability of cyclodextrin-guest complexes are therefore of considerable interest both academically and practically." MD was used to simulate cyclodextrin hydrates" as a test of the applicability of the GROMOS program package to systems beyond proteins and nucleic acids. Other early MD simulations focused on interactions with guests such as enantiomers of methyl-2-chloropropionate. Comparisons between calculated thermodynamic properties for complexes formed by O -cyclodextrin with para-substituted phenols and the results of MM simulations led to improvements in force fields that described the interactions. MM2 simulations were used to support NMR data for the -cyclodextrin inclusion complex with benzoic acid. " The well-known catalytic effect of cyclodextrins has been modeled. For example, the relative rate increase of hydrolysis of S over R phenyl ester stereoisomers in the presence of -cyclodextrin... 

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... 

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. 

Scott WRP, Hunenberger PH, Tironi IG, et al. The GROMOS biomolecular simulation program package. J Phys Chem A 1999 103 3596-3607. 

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... 

CHARMM, AMBER, GROMOS, GROMACS, Discover, and VMD/NAMD are some programs used widely to perform MD simulations (http //cmm.cit.nih.gov/modeUng/software. html). 

There are several MM force fields available, such as OPLS [29], CHARMM [30], AMBER [31], GROMOS [32], MMFF [33], CVFF [34], to mention a few. Several of them have been combined with the QM calculation programs and used in the combined QM/MM molecular dynamics simulations. [12,15,35,36] In our own work we have combined either GAUSSIAN94 [24] or GAMESS [25] with our own simulation software which is the modified version of McMOLDYN [37] package to study solvation phenomena and radical systems [38,39]. 

Dynamical simulated annealing (DSA)177 is a variant of restrained molecular dynamics (RMD).178 There are numerous programs available for performing molecular dynamics (MD) simulations, including GROMOS,178 AMBER,179 CHARMM,180 X-PLOR/CNS,181 and OPLS.182 In MD simulations, Newton s equations of motion are solved for all atoms under the influence of a physical force field ( physical), which for a protein has the form183... 

The hybrid scheme used by us has been described in detail (1). Therefore, only a short summary is given here. The system is divided into a primary (QM) part treated quantum-chemically and the environment treated by a force field (MM part). For the QM part, a semi-empirical calculation is carried out. We have used the MOPAC program (2) for this task and have, consequently, employed all NDDO methods (MNDO, AMI, PM3) in the course of our work. The interactions among atoms of the MM part are described entirely by a classical force field. They are evaluated using die GROMOS87 program (3), and the GROMOS force field or close variations of it were used in our work. 

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