[gmx-users] g_rotacf create tpr from pdb

Justin A. Lemkul jalemkul at vt.edu
Sat Aug 14 20:06:17 CEST 2010

henri mone wrote:
> 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.

Quite simply, a .tpr file can only be created by grompp.  That's exactly what 
the tutorials always say.  That's how Gromacs works.  If you conducted your 
simulation with Gromacs, you had to have had a .tpr file at some point, correct?

> 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.

The tool you want requires a .tpr file.  If you want a reason for this, look 
into the source code to see what information it's pulling.


> Looking desperately forward for an answer to my question,
> Henri
> -------
>     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"
>     file.
>     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.
> http://www.gromacs.org/Documentation/Tutorials
>     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.
> -Justin


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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