[gmx-developers] tpr format

[Xavier Periole]

>>>Hello,
>>>
>>>Is the tpr format documented anywhere (besides the source). I would like
>>>to use gromacs' geometric analysis tools for a simulation I did with
>>>NAMD. The trajectory I can convert from dcd to xtc, (is there also
>>>
>>>
>>>      
>>>
>>vmd 1.8.4 can write trajectory in trr format !!
>>    
>>
>
>I don't believe that VMD can write trajectories in trr format. I wrote
>code to convert my dcds to the xtc format to save space.
>
>
>  
>
You go in the main menu and select the molecule, then right clic your 
mouse and in the
menu choose save coordinates, a menu appears where you can select trr 
format ...

>>>documentation for the trr/trj format), but require either a tpr, tpb
>>>or tpa (what is the difference between all these?) for most of the
>>>analysis tools.
>>>
>>>
>>>      
>>>
>>For many of the analysis tools you can use a coordinate file, either gro
>>or pdb file.
>>To get a tpr file is quite easy from a pdb file if your system is a
>>protein. Adding
>>solvent would more problematic, but feasible.
>>
>>pdb2gmx -f file.pdb gives you a topol.tpr that you can use.
>>
>>    
>>
>
>Ah, so I have to go through gromacs. The problem is my system is
>coarse-grained and as a result i wanted to create the tpr file by
>hand, since I don't have an itp file that describes my system.
>  
>
It gets more complicated with coarse grain as you need to define the 
topology
to generate the tpr ...

XAvier

-- 
----------------------------------
 Xavier Periole - Ph.D.

 Dept. of Biophysical Chemistry / MD Group   
 Univ. of Groningen
 Nijenborgh 4
 9747 AG Groningen
 The Netherlands
 
 Tel: +31-503634329
 Fax: +31-503634398
 email: x.periole at rug.nl
 web-page: http://md.chem.rug.nl/~periole
----------------------------------