[gmx-users] how to interpretate a tpr file
Yang Ye
leafyoung81-group at yahoo.com
Tue Jul 11 05:52:19 CEST 2006
Dongsheng Zhang wrote:
> 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?
>
>
I think that you shall still try with your forcefield. Here is my plan:
Refer to Fig 5.3 and Fig 5.4
1. set gen-pairs in [ defaults ] as no
2. in [ nonbond_params ], enumerate all pair combination of your atoms.
Calculate their LJ or Buckingham parameters. The third column shall be 1
for LJ and 2 for Buckingham.
3. copy [ nonbond_params ] section, and rename the section name to [
pairtypes ]
*: in a complete GMX-format forcefield, 1) shall be in the ffxxxx.itp
and 2), 3) shall be in ffxxxxnb.itp.
Yang Ye
> 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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