Tags » Molecular Dynamics


K. A. Ball, J. R. Johnson, M. K. Lewinski, J. Guatelli, E. Verschueren, N. J. Krogan, and M. P. Jacobson.  “Non-degradative Ubiquitination of Protein Kinases”, PLoS Computational Biology, 12 (2016) e1004898.  PMC4890936

Molecular Dynamics

New method for rapid calculation of fundamental hydration properties

In a recent Journal of Physics: Condensed Matter Special issue on Molecular scale theories and simulations of fluid systems, Professor Tyler Luchko and his team propose a new methods for calculating small molecule hydration energy and entropy, with huge potential for… 901 more words

Journal Of Physics: Condensed Matter

Image of the week: carbohydrate binding

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

Journal Of Physics: Condensed Matter

Excited States: Bridging Scales

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

Excited State

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

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