[gmx-users] analysis using Gromacs tools

chris.neale at utoronto.ca chris.neale at utoronto.ca
Mon Feb 23 22:48:24 CET 2009

You will require a .tpr file for many analysis tools. In some cases,  
you can get away with a .ndx file. Check g_thistool -h to see what is  
mandatory input. You can make a .ndx file if you have a .pdb using  
make_ndx -f my.pdb -o my.ndx and then select your groups. If you need  
a .tpr file, then you will need a gromacs .top topology file to run  
your .pdb and .top through grompp and generate the .tpr. Generating  
your .top may be simple if you have a simple system. Try downloading  
the amber forcefield that is formatted for gromacs and running your  
.pdb through pdb2gmx while selecting that amber ff in order to  
generate a .top file.

Note that if you need a .tpr file this is all going to require that  
you learn how to use gromacs and will not be completed in one afternoon.

The gromacs manual is quite good.


-- original message --

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 using  
Gromacs tools ? or Will I have to have some other files for analysis  
in Gromacs ?  I?m waiting for your suggestions and helps.

Thank you very much for your attention.


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