Simulaid performs a large number of simulation-related tasks: interconversion and modification of structure and trajectory files, optimization of orientation, and a large variety of analysis functions. The program can handle structures in PDB (Berman et al., Nucleic Acids Res 2000, 28, 235), Charmm (Brooks et al., J Comput Chem 4, 187) CRD, Amber (Case et al.), Macromodel (Mohamadi et al., J Co...

The fully hydrated liquid crystalline phase of the dimyristoylphosphatidycholine lipid bilayer at 30 degrees C was simulated using molecular dynamics with the CHARMM potential for five surface areas per lipid (A) in the range 55-65 A(2) that brackets the previously determined experimental area 60.6 A(2). The results of these simulations are used to develop a new hybrid zero-baseline structural ...

In this study, the interactions of two effective derivatives methotrexate anticancer drug with Single-wall carbon nanotubes (SWNTs) and Boron nitride (BNNTs) in gas phase were investigated using DFT calculations. Through method, effects different solvents on interaction SWNTs BNNTs within Onsager self-consistent reaction field (SCRF) model, as well temperature stability between compounds variou...

This paper presents an approach for deriving 3-D structures of polypeptide chains which have minimum energy. The well-known optimisation algorithms are usually applied on the model which contains hard constraints over coordinates of the atoms. The drawback of such strategies is an ineecient search for the optimal solution. Our approach proceeds in two steps: rst, the standard model is transform...

Quantitative free energy computation involves both using a model that is sufficiently faithful to the experimental system under study ~accuracy! and establishing statistically meaningful measures of the uncertainties resulting from finite sampling ~precision!. We use large-scale distributed computing to access sufficient computational resources to extensively sample molecular systems and thus r...

A lesson utilizing a coarse-grained (CG) Gō-like model has been implemented into the CHARMM INterface and Graphics (CHARMMing) web portal (www.charmming.org) to the Chemistry at HARvard Macromolecular Mechanics (CHARMM) molecular simulation package. While widely used to model various biophysical processes, such as protein folding and aggregation, CG models can also serve as an educational tool ...

We examine the use of truncated singular value decomposition and Tikhonov regularization in standard form to address ill-posed least squares problems Ax = b that frequently arise molecular mechanics force field parameter optimization. illustrate these approaches by applying them dihedral optimization genotoxic polycyclic aromatic hydrocarbon-DNA adducts are interest study chemical carcinogenesi...

We compare the conformational distributions of Ace-Ala-Nme and Ace-Gly-Nme sampled in long simulations with several molecular mechanics (MM) force fields and with a fast combined quantum mechanics/molecular mechanics (QM/MM) force field, in which the solute's intramolecular energy and forces are calculated with the self-consistent charge density functional tight binding method (SCCDFTB), and th...