[gmx-users] dihedral parameters in oplsaa
friendli
friendli2000 at gmail.com
Tue May 27 11:16:09 CEST 2008
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 ; **.
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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