Instantaneously generation of random numbers
Posted: February 5, 2008 Filed under: bash, geek, scripting Leave a comment »#! /bin/bash
coff=1.2
nnce=765
cent=cl_$coff.centers
seed=`date +'%N'`
awk 'BEGIN{
srand("'$seed'")
print int(rand())
}'
Trajectory overlay with VMD
Posted: January 29, 2008 Filed under: clusterization, geek, vmd 1 Comment »In Molecular Dynamics, especially when small fluctuations are involved, it can be helpful to display the snapshots contained in a trajectory all at once instead of viewing a movie. The same utility can be used, for example, to display the members of a structural cluster (you can generate clusters of structures using wordom).
This feature is usually achieved “by hand”, e.g., extracting all the snapshots of a trajectory into separate pdb files and then loading them all at once. A simple consequence of this, of course, is to have your hard-drive overfilled with redundant files.
Good for us, VMD is able to overlay in a single frame all the snapshots contained in your trajectory (thanks Riccardo for your message). Once your trajectory is loaded in (from command line):
vmd -f trj.dcd prot.psf
go to:
Graphics>Representations>Trajectory
in the field “Draw Multiple Frames” replace “now” with x:y:z where x is the first frame to display (starting from 0), y is the skip step, and z is the last displayed frame. In the case of a trajectory of 50 frames I would write something like:
1:1:50
That’s it! Your trajectory is overlayed.
Wordom: a program for efficient analysis of molecular dynamics simulations
Posted: August 27, 2007 Filed under: geek, papers Leave a comment »Seeber M, Cecchini M, Rao F, Settanni G, and Caflisch A. Bioinf. (2007) doi:10.1093/bioinformatics/btm378
