[gmx-users] how to interpretate a tpr file

[Dongsheng Zhang]

On Mon, 2006-07-10 at 13:58 +0800, Yang Ye wrote:
> 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.

my questions is how gromacs makes the association, especially for the LJ
potential between two different atoms. Do you mean atom type in:

 atom[     0]={type=  0, typeB=  0, ptype=    Atom, m= 1.20110e+01, q=
0.00000e+00, mB= 1.20110e+01, qB= 0.00000e+00, resnr=    0} grpnrs=[ 1 1
0 0 0 0 0 0 0 0 ]}

The number 0 in "type=  0" is an index number for different atoms in the
top file. It doesn't match with i in " functype[i] ". 

If you want me to check the source code, could please tell which portion
of the source code can answer my question? I have checked sim_util.c,
but haven't found the answer.

Thank you for your help!


> >   
> >>> 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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