[gmx-users] dihedral parameters in oplsaa
David van der Spoel
spoel at xray.bmc.uu.se
Tue May 27 11:17:21 CEST 2008
friendli wrote:
> Thanks David and Mark for the advice. But I think I did not state it
> very clearly.
>
> It is not 9 sets of dihedrals which share the same parameters are found
> in the output by gmxdump. But 9 of the 15 dihedrals exist in this
> molecule are listed. They are under Ryckaert-Bell. As for the function
> types, there are only two.
>
> I pastes the relevant part this time. The missing parameter dihedrals
> are labeled with ; **.
Then most likely they have parameters that are zero. Do you get grompp
warnings about this?
>
> from .top file,
> [ dihedrals ]
> ; ai aj ak al funct c0 c1
> c2 c3 c4 c5
> 2 1 5 6 3
> 2 1 5 7 3
> 2 1 5 8 3
> 3 1 5 6 3
> 3 1 5 7 3
> 3 1 5 8 3
> 4 1 5 6 3
> 4 1 5 7 3
> 4 1 5 8 3
> 1 5 8 9 3 ; **
> 1 5 8 10 3 ; **
> 6 5 8 9 3 ; **
> 6 5 8 10 3 ; **
> 7 5 8 9 3 ; **
> 7 5 8 10 3 ; **
> ___________________________________________
> from gmxdump,
> Ryckaert-Bell.:
> nr: 45
> multinr[division over processors]: 45
> iatoms:
> 0 type=47 (RBDIHS) 1 0 4 5
> 1 type=47 (RBDIHS) 1 0 4 6
> 2 type=48 (RBDIHS) 1 0 4 7
> 3 type=47 (RBDIHS) 2 0 4 5
> 4 type=47 (RBDIHS) 2 0 4 6
> 5 type=48 (RBDIHS) 2 0 4 7
> 6 type=47 (RBDIHS) 3 0 4 5
> 7 type=47 (RBDIHS) 3 0 4 6
> 8 type=48 (RBDIHS) 3 0 4 7
> _____________________________________________
> for identify the atom numbers,
> [ atoms ]
> ; nr type resnr residue atom cgnr charge mass
> typeB chargeB massB
> 1 opls_287 1 GLY N 1 -0.3 14.0067 ;
> qtot -0.3
> 2 opls_290 1 GLY H1 1 0.33 1.008 ;
> qtot 0.03
> 3 opls_290 1 GLY H2 1 0.33 1.008 ;
> qtot 0.36
> 4 opls_290 1 GLY H3 1 0.33 1.008 ;
> qtot 0.69
> 5 opls_298 1 GLY CA 1 0.09 12.011 ;
> qtot 0.78
> 6 opls_140 1 GLY HA1 1 0.06 1.008 ;
> qtot 0.84
> 7 opls_140 1 GLY HA2 1 0.06 1.008 ;
> qtot 0.9
> 8 opls_271 1 GLY C 2 0.7 12.011 ;
> qtot 1.6
> 9 opls_272 1 GLY O1 2 -0.8 15.9994 ;
> qtot 0.8
> 10 opls_272 1 GLY O2 2 -0.8 15.9994 ;
> qtot 0
>
>
> regards
>
> LQ
>>
>> Message: 7
>> Date: Tue, 27 May 2008 13:54:08 +0800
>> From: friendli <friendli2000 at gmail.com>
>> Subject: [gmx-users] dihedral parameters in oplsaa
>> To: gmx-users at gromacs.org
>> Message-ID: <483BA200.1040704 at gmail.com>
>> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>>
>> Hi gmx users,
>>
>> In order to understand the oplsaa all atom force field, I use pdb2gmx
>> to generate topology file of a pdb which contains only one AA( the
>> glycine).
>>
>> After the EM simulation, I use gmxdump to look for the details of the
>> parameters.
>>
>> I find,
>> in .top file, there are 15 proper dihedrals under directive
>> [dihedrals] and the funtion type is 3 (i.e. RB dihedrals).
>> However, in the output generated by gmxdump, there are explicit
>> parameters for only 9 of these dihedrals. The 9 dihedrals corresponds
>> to 9 of the 15 in .top correctly, but the other 6 are missing.
>>
>> In the six missed dihedrals, two are for N-CA-C-O, four are for
>> HA-CA-C-O.
>>
>> Can anybody give a hint on this? Is there any default value not output
>> by gmxdump? All other parameters are fully printed.
>>
>>
>> H H O
>> | | | H- N - C - C = O
>> |
>> H
>>
>> thank you
>>
>> LQ
>>
>>
>> ------------------------------
>>
>> Message: 8
>> Date: Tue, 27 May 2008 08:21:55 +0200
>> From: David van der Spoel <spoel at xray.bmc.uu.se>
>> Subject: Re: [gmx-users] dihedral parameters in oplsaa
>> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>> Message-ID: <483BA883.6030703 at xray.bmc.uu.se>
>> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>>
>> friendli wrote:
>>
>>> Hi gmx users,
>>>
>>> In order to understand the oplsaa all atom force field, I use pdb2gmx
>>> to generate topology file of a pdb which contains only one AA( the
>>> glycine).
>>>
>>> After the EM simulation, I use gmxdump to look for the details of the
>>> parameters.
>>>
>>> I find,
>>> in .top file, there are 15 proper dihedrals under directive
>>> [dihedrals] and the funtion type is 3 (i.e. RB dihedrals).
>>> However, in the output generated by gmxdump, there are explicit
>>> parameters for only 9 of these dihedrals. The 9 dihedrals
>>> corresponds to 9 of the 15 in .top correctly, but the other 6 are
>>> missing.
>>>
>>> In the six missed dihedrals, two are for N-CA-C-O, four are for
>>> HA-CA-C-O.
>>>
>>> Can anybody give a hint on this? Is there any default value not
>>> output by gmxdump? All other parameters are fully printed.
>>>
>>>
>>> H H O
>>> | | | H- N - C - C = O
>>> |
>>> H
>>>
>>
>> multiple dihedrals share the same parameters. look further down at
>> RBDIHS.
>>
>>> thank you
>>>
>>> LQ
>>> _______________________________________________
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>>>
>> Message: 9 Date: Tue, 27 May 2008 17:45:02 +1000 From: Mark Abraham
>> <Mark.Abraham at anu.edu.au> Subject: Re: [gmx-users] dihedral parameters
>> in oplsaa To: Discussion list for GROMACS users
>> <gmx-users at gromacs.org> Message-ID: <483BBBFE.5090101 at anu.edu.au>
>> Content-Type: text/plain; charset=ISO-8859-1; format=flowed friendli
>> wrote:
>>> > Hi gmx users,
>>> > > In order to understand the oplsaa all atom force field, I use
>>> pdb2gmx to > generate topology file of a pdb which contains only one
>>> AA( the glycine).
>>> > > After the EM simulation, I use gmxdump to look for the details of
>>> the > parameters.
>>> > > I find,
>>> > in .top file, there are 15 proper dihedrals under directive
>>> [dihedrals] > and the funtion type is 3 (i.e. RB dihedrals).
>>> > However, in the output generated by gmxdump, there are explicit >
>>> parameters for only 9 of these dihedrals. The 9 dihedrals
>>> corresponds > to 9 of the 15 in .top correctly, but the other 6 are
>>> missing.
>>> > > In the six missed dihedrals, two are for N-CA-C-O, four are for
>>> > HA-CA-C-O.
>>> > > Can anybody give a hint on this? Is there any default value not
>>> output > by gmxdump? All other parameters are fully printed.
>>> > > > H H O
>>> > | | | H- N - C - C = O
>>> > |
>>> > H
>>>
>> Well done for using your initiative to see how things work :-) As
>> David said, each unique function is only stored once. Later in the
>> gmxdump there's another field that has an entry for each atom number
>> involved in an actual dihedral, and an index into this table of 9
>> dihedral functions to actually look up the parameters. Also, do be
>> aware that gmxdump numbers beginning from 0, but your .top begins from
>> 1. Mark
>>
>
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--
David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
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