[gmx-users] how to interpretate a tpr file

[Yang Ye]

Dongsheng Zhang wrote:
> Yang Ye,
>
> Thank you very much for your help. I still have some questions:
>
> On Mon, 2006-07-10 at 11:35 +0800, Yang Ye wrote:
>   
>> 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.
>>     
>  Is this exclusion for nonbonded interactions, including 1-2, 1-3
> interactions? If so, I don't understand why there are 17 atoms to be
> excluded for atom 0. It is a capped carbon nanotube. Each C has three
> single covalent bond, so the total exluded atoms for each atom should be
> 6.
>
> This is next term for exlusion:
>
> excl[1][18..35]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 
>                13, 14, 15, 20, 22}
> Why are there two different exclusions for atom 0?
>   
Please check your top file, including those files included into it. 
Remove/Change some and compare the dump.
>>> 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...
>>     
> Anyone can help me for this one? Thanks!
>
>   
>>> 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.
>>     
>
> I am sorry I am not clear here. I know C6 and C12 is for the LJ
> interaction between C and C in nanotube by looking at **nb.itp file. How
> can gromacs know it in tpr file (I believe all information should be in
> tpr file)? Let me give you an example. In tpr file, type=81 (ANGLES)
> 1041 1040 1042 shows that the angle bending parameters for atoms  1041
> 1040 1042 are from functype[81], but I can't find any information which
> says  the LJ parameters for C and C are from functype[0].
>   
mdrun will associate functype[i] with atom type. check gmx source code 
if you are still not sure.
>   
>>> 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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>>>   
>>>       
>>
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