Tags » Molecular Dynamics

Membrane Induced Folding of a cationic ß-hairpin

We recently developed a minimalistic coarse-grained model for lipids and peptides by using the Drude oscillator approach to model the  electrostatic component of Hydrogen bonds. With our models, we were able to simulate membrane induced folding of a cationic ß-hairpin, SVS-1 on… 93 more words

Molecular Dynamics

Energy component analysis for OpenMM

OpenMM has been gaining popularity because of the flexibility it offers for scientists to implement new methodologies and force fields. But it is still not straightforward enough to give you the energy contributions from each component of force-field. 78 more words

Computational Chemistry

Calculate RESP Charge in antechamber

assalamu’alaikum warahmatullahi wabarakatuh..

kali ini kita akan membahas bagaimana menghitung muatan RESP menggunakan antechamber. langkahnya sangat sederhana yaitu : pertama-tama optimasi dulu menggunakan Gaussian kemudian outputnya dimasukkan ke dalam antechamber 94 more words

Kimia Komputasi

Water Transport in Membranes

Here is a movie I made today, it shows water transport through a membrane inserted peptide. All the colored beads represent lipid head groups, the peptide backbone is in black, the orange beads represent LYS side chains and the cyan bead is a water. 49 more words

Molecular Dynamics

Music of the Macromolecules

To fully understand a molecule, you first need to learn what it looks like, and then, how it moves. This isn’t easy. I’ve talked before… 2,134 more words


7.1 Statistical Physics: Molecular Boxing - Microcanonical ensamble vs Quasi-molecular dynamics

Let me reuse previously developed model of particles in the box. Today I would like to simulate statistical microcanonical ensemble of non-interacting particles(Ideal Gas). The main aim is to determine whether the macroscopic quantities like temperature or pressure obtained via averaging over… 149 more words