[gmx-users] 3.3 release and Forcefield nb.itp format

[Erik Lindahl]

Hi Yang,

You might indeed be right. Since you already have a testsystem - it  
would be great if you could file it as a bug in bugzilla.gromacs.org,  
and I'll fix it before releasing 3.3.1.

Cheers,

Erik

On Oct 18, 2005, at 8:53 PM, Yang Ye wrote:

> no. I suspect there is a bug in grompp. I have specified comb-rule  
> 3 for my FF but grompp used rule 1.
>
> Yang Ye
>
> David wrote:
>> On Wed, 2005-10-19 at 02:34 +0800, Yang Ye wrote:
>>
>>> After checking, I found that grompp has used comb-rule 1 for
>>> generating LJ.
>>>
>> So problem solved?
>>
>>
>>
>>> Yang Ye
>>>
>>> [ defaults ]
>>> ; nbfunc        comb-rule       gen-pairs       fudgeLJ fudgeQQ
>>>    1            3               no                0.5   0.833333
>>>
>>> Erik Lindahl wrote:
>>>
>>>> Hi Yang,
>>>>
>>>> Please include the header [defaults] section from your forcefield.
>>>>
>>>> The number of columns is flexible, since both atomic number and
>>>> bonded_atomtype fields are optional.
>>>>
>>>> Cheers,
>>>>
>>>> Erik
>>>>
>>>> On Oct 18, 2005, at 7:25 PM, Yang Ye wrote:
>>>>
>>>>
>>>>> Hi,
>>>>>
>>>>> I have found that 3.3's grompp generates drastically different
>>>>> LJ_SR and LJ14 parameters for one of my self-defined forcefield
>>>>> (converted from AMBER).
>>>>>
>>>>> >From gmxdump,
>>>>> (3.3's tpr) tpx version 40
>>>>>         ntypes=72
>>>>>            functype[0]=LJ_SR, c6= 2.24468820e-20, c12=
>>>>> 3.18825866e-35
>>>>>            functype[1]=LJ_SR, c6= 1.61870333e-32, c12= 0.00000000e
>>>>> +00
>>>>>            functype[2]=LJ_SR, c6= 1.43123863e-20, c12=
>>>>> 1.22953165e-35
>>>>>            functype[3]=LJ_SR, c6= 1.17580789e-26, c12= 0.00000000e
>>>>> +00
>>>>>            ...
>>>>>
>>>>> They should be
>>>>> (3.3b's tpr) tpx version 32
>>>>>         ntypes=72
>>>>>            functype[0]=LJ_SR, c6= 3.35273775e-03, c12=
>>>>> 3.95092275e-06
>>>>>            functype[1]=LJ_SR, c6= 8.76983977e-05, c12=
>>>>> 8.89523299e-09
>>>>>            functype[2]=LJ_SR, c6= 3.08322068e-03, c12=
>>>>> 4.16509010e-06
>>>>>            functype[3]=LJ_SR, c6= 4.73846623e-04, c12=
>>>>> 2.59686658e-07
>>>>>            ...
>>>>>
>>>>> My ffambernb.itp is
>>>>> [ atomtypes ]
>>>>> ;name        mass      charge   ptype            c6           c12
>>>>>     H     1.008     0.000     A  3.9229141156e-07
>>>>> 5.8568793913e-13
>>>>>    HO     1.008     0.000     A  0.0000000000e+00  0.0000000000e
>>>>> +00
>>>>> ...
>>>>> [ nonbond_params ]
>>>>> ; i    j func          c6           c12
>>>>>     H     H   1  3.9229141156e-07  5.8568793913e-13
>>>>>     H    HO   1  0.0000000000e+00  0.0000000000e+00
>>>>>     H    HS   1  3.9229141156e-07  5.8568793913e-13
>>>>> ...
>>>>> [ nonbond_params ]
>>>>> ; i    j func          c6           c12
>>>>>     H     H   1  3.9229141156e-07  5.8568793913e-13
>>>>>     H    HO   1  0.0000000000e+00  0.0000000000e+00
>>>>>     H    HS   1  3.9229141156e-07  5.8568793913e-13
>>>>> ...
>>>>>
>>>>> I found that FF provided by gromacs has different column width. Is
>>>>> this the reason?
>>>>>
>>>>> Thanks.
>>>>>
>>>>> Yang Ye
>>>>>
>>>>> _______________________________________________
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>>>>>
>>>>>
>>>>>
>>>> -----------------------------------------------------------
>>>> Erik Lindahl  <lindahl at sbc.su.se>
>>>> Assistant Professor, Stockholm Bioinformatics Center
>>>> Stockholm University, SE 106 91 Stockholm
>>>> Phone: +46 8 5537 8564     Fax: +46 8 5537 8214
>>>>
>>>>
>>>>
>>>>
>>>> _______________________________________________
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>>>>
>>>>
>>> -- 
>>> Regards,
>>> Yang Ye
>>> Computational Biology Lab
>>> School of Biological Sciences
>>> Nanyang Technological University
>>> Singapore
>>> Tel: 6316-2884
>>>
>>> _______________________________________________
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-----------------------------------------------------------
Erik Lindahl  <lindahl at sbc.su.se>
Assistant Professor, Stockholm Bioinformatics Center
Stockholm University, SE 106 91 Stockholm
Phone: +46 8 5537 8564     Fax: +46 8 5537 8214




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