Re: about trajectory analysis

From: Nicholas M Glykos (
Date: Wed May 30 2012 - 02:06:56 CDT

> I want to ask some questions about trajectory analysis. I have some md
> simulation output files that includes coordinate, force and velocity
> information. And these files are huge ( more than 5 GB ) . Could you
> please recommend a free text editor which works on Linux or Windows to
> open and editthese huge files?

Have these been produced by NAMD ? The DCD file format is binary, which
means that (i) normal humans can't edit them with a text editor (but
hexedit would do), (ii) because these are the result of your simulation,
you should analyse them, not 'edit' them. Google for 'molecular dynamics
analysis software'. Most people use programs like VMD and/or the tools
from the gromacs suite.

> And I will run these files with fortran codes and get again huge output
> files. In order to do this operation faster and seamlessly what should
> I do ?

Too vague. If you already know which programs you'll use for the analysis,
and if these programs can read and process your trajectory files, then you
are set to go. How could anyone tell you how to make an unspecified
fortran code go faster with some unspecified trajectory files (and for
some unspecified analyses) ?

            Nicholas M. Glykos, Department of Molecular Biology
     and Genetics, Democritus University of Thrace, University Campus,
  Dragana, 68100 Alexandroupolis, Greece, Tel/Fax (office) +302551030620,
    Ext.77620, Tel (lab) +302551030615,

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