[gmx-users] how to interpretate a tpr file

[Yang Ye]

Dongsheng Zhang wrote:
> Dear GMX users:
>
>
> Could someone help me to understand these information from a position
> restrained tpr file?
>
> 1.   excl[0][0..17]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 13, 14, 15,     
>                      16, 18, 26, 28}
>   
Exclusion group 0, there are total 17 exclusions in this group. between 
0 (the first one) and remaining 17 atoms.
> 2.   blocks[CGS][0][0..19]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 
>                12, 13, 14, 15, 16, 17, 18, 19}
>
> 3.   blocks[MOLS][2][1802..1805]={1802, 1803, 1804, 1805}
>   
Both are useful for dividing the atoms for parallel processing (before 
domain decomposition arrives in gmx 4.0 :-).
CGS means charge group. MOLS means molecules. Division shall not break 
one charge group or a molecule (hope that I am not wrong here).
> 4.   blocks[SBLOCKS][0][0..1039]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 
>                10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 
>                24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 
>                38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 
>                52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64,  
>                65, ........... 1039}
>   
Not sure...
> 5.  functype[0]=LJ_SR, c6= 5.72640402e-03, c12= 1.86486031e-05
>  I know this is for the parameters of LJ potential. My question is where
> is the information that tells gromacs to use these parameters for the
> interaction between two specific atoms.
>   
see atoms: section; type there refers to the functype here. Any functype 
number for LJ_SR beyond the atom number there will not be used.
> As someone has suggested, if gromacs website can offer the
> interpretation for each file, I believe many people will highly
> appreciate it.
>
> All the best!
>
> Dongsheng
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