[gmx-users] how to interpretate a tpr file
Dongsheng Zhang
dong at pampas.chem.purdue.edu
Mon Jul 10 20:33:33 CEST 2006
Yang Ye,
Thank you very much!
Do you know if there is any reason for gromacs to prevent using both LJ
and Buckingham potential for nonbonded interaction between different
atoms? I have a force field which includes an attractive part of
Buckingham potential for h-bond (All other nonbonded interactions are
LJ). If you think it is OK to use two types of nonbonded interactions (I
prefer it), could you please tell me how I can modify the source code?
All the best!
Dongsheng
On Tue, 2006-07-11 at 01:53 +0800, Yang Ye wrote:
> Longshoremen Zhang wrote:
> > 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] ".
> >
> I take one small system as an example. I got 126 atoms. So I have
> following lines in my dump file for tpr.
>
> topology:
> name="GGCC"
> atoms:
> atom (126):
> ...
>
> From the atom list below, the largest number in type is 12. So I have
> 13 types of atoms.
>
> In the later sections of the dump file, I have
>
> idef:
> catnap=13
> nodeid=0
> ntypes=296
>
> Notice that here atnr=13. atnr means atom type number.
>
> functype[0] to functype[168] are for LJ_SR (169 lines, so 169 sets
> parameters c6, c12). So they are the all possible combination of the LJ
> interaction parameters between any two types of atom. 13*13 = 169. Exact
> order of them can be interpreted by recalculation.
>
> Yang Ye
> > 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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