Gradient RMS

Enter RMS Gradient per Atom Criterion [0.01] Enter (this is the default option)... 

For multi-dimensional potential energy surfaces a convenient measure of the gradient vector is the root-mean-square (RMS) gradient described by... 

A line minimization is performed along the conjugate direction hj until a minimum is found that defines the next point, where the gradient is re-evaluated as gj+i. If the RMS gradient is below the convergence threshold the procedure is terminated, otherwise ... 

The RIPS conformational search starts by perturbing all of the atoms X, Y, and Z coordinates by plus or minus the perturbation value (usually 2 A or less) the sign ( ) is randomly assigned. Next the molecule is energy minimized to a user-defined RMS gradient requirement. After each molecule is minimized, a check is preformed for a duplicate conformation existing in the conformer list. If the current structure is a new conformation, it is added to the list and the failure count (number of times a conformation that exists in the conformer list is repeated) is set to zero. A duplicate conformer is discarded and the failure count is increased by one. The search is considered complete once the number of failures has reached the user-defined values. 

Click Start to initiate docking computation, which terminates when either RMS error or RMS gradient becomes less than the set values. 

Choose algorithm such as Steepest descent, Fletcher-Reeves (conjugate gradient), or Polak-Ribiere (conjugate gradient, default of FlyperChem), and choose options for termination condition such as RMS gradient (e.g., 0.1 kcal/mol A) or number of maximum cycles. 

Perform geometry optimization until RMS gradient is equal to or less than 0.100. Formulate your conclusions with reference to their interaction energies. 

Deduce the probable conformation of porcine glucagon with the following sequence (construct initial structure in a helix from amino acids with HyperChem which lists residue ID in PDB file) by geometry optimization until the difference in energies between the successive steps is less than 1.0 kcal/mol or rms gradient of 0.1 kcal/(mol-A) ... 

Compute -F properties. The initial model shows total energy (Et) of 29895.86 kcal/mole and RMS gradient (RMSG) of 7108kcal/A-mole... 

Energy minimization, ccmformational searching and molecular mechanics were performed using Alchemy 2000 program system from Tripos loaded on a PC Pentium Computer. For molecular mechanics optimization, the MM3 Molecular Mechanics siAroutine with a value of 4.7 for dimethyl formamide dielectric constant, a RMS gradient of 0.05 kCai/A mot and a delta of energy of 0.001 kCai/A was used. 

Intel mO Cliates None Medium Fine RMS Gradient [ i ... 

Final Moilel [ None 1 Medium 1 Fine RMS Gradient 0. S ... 

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