[gmx-users] g_rotacf create tpr from pdb

henri mone henrimone at gmail.com
Sat Aug 14 20:01:46 CEST 2010

Der Gromacs users and dear Justin,

The gromacs tutorial does not really tell how to create a "tpr"
without a "mdp" file. The standard procedure in the tutorials is to
use the program "grompp" which always requires a "mdp" file. But for
calculating the autocorrelation function I only need the coordinates
of my system and noting else.

I still don't understand why the program "g_rotacf" needs additional
information beside the pdb and the xtc trajectory. To calculate the
autocorrelation three atoms are required. The two distance vector
between this three atoms are calculated. The vector product gives the
corresponding normal vector. For this normal vector the
autocorrelation is calculated.
In the entire algorithm nothing beside the coordinates is required.

Looking desperately forward for an answer to my question,

    Dear Gromacs experts and newbies,

    The program "g_rotacf" (calculates the autocorrelation function)
    requires as input for the -s option either a "tpr", "tpb" or "tpa"
    I does not accept for the -s option a PDB file :- ( .
    How can I create from a "pdb" file a "tpr" file?
    The program "pdb2gmx" can only create from a  "pdb a "top" or  "gro"
    file but no "tpr" file.
    I also tried "grompp" but this needs a "mdp" file.

    Making it short here are my two questions:
    1. How do I create for "g_rotacf" a  "tpr", "tpb" or "tpa" file?

Please consult any basic tutorial to get a grasp for a basic Gromacs workflow.


    2. "g_rotacf" only extracts the coordinates from the xtc trajectory
    why does it need a topology file (via  "tpr", "tpb" or "tpa").

Probably because it needs some type of information not stored in .pdb
files - bonds, masses, PBC information, etc.


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