dalvarez's blog


Organic solvent boxes

Due to the demand to use the organic/water mixtures published in the MDMix work done in our group, here you can download two preequilibrated boxes:
  • ETAWAT20 (ethanol 20% concentration)
  • ISOWAT20 (isopropanol 20%). 
These boxes are saved in Amber Object File format. Prepared to work with tLeap or xLeap from Amber software.

HDD Health monitoring

Useful tool for monitoring and checking HDD health on a linux machine:


Parallel Programming in Python

I found today an interesting python package that permits to set up very easily a parallel computing script. I had a python script that analyzes a molecular dynamics trajectory and it was taking almost 60 seconds per snapshot. And it was not feasable to analyze thousands of them at this speed. Si googling a bit, i found this processing python package (http://pyprocessing.berlios.de/). I could install it as simple as running:

Salty high concentration MDs

It has been described a bad modelling parameters for some ions in the AMBER FF. In simulations with high concentration of these ions, they tend to aggregate instead of remaining totally disolved (as expected at the concentrations worked).

This paper describes this fenomena and gives new parameters that improve the behaviour of these atoms: Cheatham's JPCB 2008

Extract equilibrium distance for two atom types from Amber Topology File. Accurate Contacts Calculations.

It might be sometimes interesting to know the equilibrium distance between two atom types.

Using NAMD with harmonic restraints

In this post I will explain how to restraint the whole protein for running a MD using NAMD.

For applying harmonic restraints in NAMD we need to generate a PDB file of the system in which we indicate the atoms that we want to be restrained and the force to be applied.

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