[gmx-users] analysis using Gromacs tools

Mark Abraham Mark.Abraham at anu.edu.au
Mon Feb 23 23:17:42 CET 2009

oguz gurbulak wrote:
> Dear All,
> I'm planning to use Gromacs  for analysis with Amber trajectory files ( 
> mdcrd, rst files ). And I found a script that converts Amber mdcrd files 
> to *Gromacs-compatible .xtc *files. I want to learn that if 
> *Gromacs-compatible .xtc *files are enough to perform an analysis 
> <http://www.tureng.com/search/perform+an+analysis> using Gromacs tools ? 

"Analysis" is too vague a description to get a useful answer. Some 
GROMACS analysis tools will be fine with just your trajectory file, some 
will require atom names that could come from a PDB or .tpr file, some 
will require atom types and/or connectivity that must come from a .tpr 
file. This goes for AMBER too!

> or Will I have to have some other files for analysis 
> <http://www.tureng.com/search/perform+an+analysis> in Gromacs ?  I’m 



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