Molecular recognition is an integral part of many biological reactions. This week’s image comes from a paper by Shoichi Tanimoto et al who use molecular dynamics and the 3D reference interaction site model (3D-RISM) method to examine the ion dependancy of carbohydrate binding in the carbohydrate-binding module family 36 (CBM36). 69 more words
Tags » Molecular Dynamics
Miquel, Nicolas and I are organizing a workshop in Marseille this November.
This workshop will bring together specialists from different computational fields to discuss simulations of excited-state molecular and supra-molecular phenomena occurring in diverse scales. 22 more words
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
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
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
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