Molecular dynamics GROMOS

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... 

AMBER, GROMOS, QUANTA/CHARMm molecular dynamics (see text)... 

GROMOS A general-purpose molecular dynamics computer simulation package for the study of biomolecules http //igc.ethz.ch/gromos/weicome.htmi GROMACS (GROningen MAchine for Chemical Simulations) http //rugmdO. chem. rug.ni/ gmx/... 

Tapia O, Velasquez I (1997) Molecular Dynamics Simulations of DNA with Protein s Consistent GROMOS Force Field and the Role of Counterions Symmetry, J Am Chem Soc, 119 5934... 

Molecular Dynamics Simulation of the Proline Conformational Equilibrium and Dynamics in Antamanide Using the GROMOS Force Field. 

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 model was built and optimized in the absence of inhibitors. Dipeptide inhibitors were docked in the eneigy-minimized model. The coordinates of the slowly hydrolyzed substrate glycyl-L-tyrosine [114] for CPA were used to guide the (manual) docking. Atomic coordinates were obtained from the Protein Data Bank [115], Energy minimization and molecular dynamics were carried out with GROMOS [116]. 

Thompson S M 1983. Use of Neighbour Lists in Molecular Dynamics. CCP5 Quarterly 8 20-28. van Gunsteren W F and H J C Berendsen 1986. GROMOS User Guide. 

Stephenson G 1973 Mathematical Methods for Science Students. London, Longman Swaminathan S, G Ravishanker and D L Beveridge 1991. Molecular Dynamics of B-DNA Including Water and Counterions - A 140-ps Trajectory for d(CGCGAATTCGCG) Based on the Gromos Force Field Journal of the American Chemical Society 113-5027-5040... 

There are several software packages available that perform molecular dynamics simulations, such as AMBER,S9 CHARMM, SYBYL, DISCOVER, and GROMOS. 3 These programs are written to facilitate the simulation of peptides and proteins in vacuo and in solution. Because of the CPU time required to carry out these simulations, programs that run on a PC are not plentiful. However, HyperChem does provide for molecular dynamics using an IBM PC (or compatible) with the 80386 or 80486 microprocessor. Molecular dynamics of small molecules can be done using Chem3D Plus. The user who... 

Van der Waals interactions are proportional to 1/Rfj at large distances and so are short range. A van der Waals cutoff distance of 8 A is typically used and was believed to produce little error. However, molecular-dynamics simulations of liquid alkanes using the GROMOS force field found that the enthalpies of vaporization and the vapor pressures changed very substantially when the van der Waals cutoff distance was varied within the range 8 to 14 A, and so a van der Waals cutoff radius of 16 A is much more justifiable than the traditional one of 8 A [X. Daura et al., J. Comput. Chem., 19, 535 (1998)]. 

Molecular modeling and computer simulation with empirical potential energy function (force field) are now routinely carried out to help understand and predict structures and dynamics of proteins and other macromolecules of biological relevance in water and membrane environments. After over 40 years of development, popular force fields such as AMBER, CHARMM, OPLS and GROMOS have been widely employed in biomolecular simulations. These force fields are used dominantly in highly optimized molecular dynamics... 

Fig. 8.3 Free energy profiles along the S-S -C-C dihedral angle of the disulfide bridge of the 127 protein as a function of external force. The profile has been obtained from force-field molecular dynamics simulations carried out with GROMOS at r = 300 K. The model system in these simulations comprises the 127 protein and SPC water molecules solvating the protein in a tetragonal box. The relevant S-S-C-C conformers of the disulfide bridge embedded in the protein are shown on top using a partial and schematic representation. Courtesy of Padmesh Anjukandi...

Driesner et al have recently performed a molecular dynamics study of the hydration and ionic association in the archetypal NaCl aqueous system (based on GROMOS force fields [224]), from infinite dilution to 1 molal and from ambient to supercritical conditions [225]. They concluded that, for infinitely dilute solutions, the... 

The relevant literature on lactose dissolution in water has been reviewed in a paper which describes a mathematical model for this process/ Short time scale molecular dynamics simulations of sucrose in water and DMSO indicated that the conformations in both solvents are similar to that accepted in the crystalline state/ Solid-liquid equilibria for aqueous sucrose have been studied by use of an UNIQUAC model/ A comparison of GROMOS force field and Ha force field in molecular dynamics simulations of glucose crystals indicated superior performance by the latter method/ Predicted crystal structures of P-D-glucose, P-D-galactose, P-D-allose, a-D-glucose, a-D-galactose, and a-D-talose matched or nearly matched the X-ray-derived data in four cases/ ... 

Once at the desired temperature, the molecule is allowed to equilibrate at that temperature for 10-20 picoseconds before allowing the simulation to "run free," at which time various molecular properties such as geometry and overall energy can be monitored as a function of time. All molecular dynamics simulations discussed herein made use of the GROMOS software package, authored by van Gunsteren, et al [30]. 

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