[gmx-users] ForceField of ethanol and the default parameters in Gromacs

[Mark Abraham]

Hi,

On Fri, Aug 18, 2017 at 6:14 AM ZUO Taisen <zuots at ihep.ac.cn> wrote:

>  Dear Gromacs developer:
>
>        There is a topology file of ethanol in the OPLS FF of the new
> version of Gromacs (Gromacs2016 please see bellow). However, I did not see
> any bond, angle or dihedral parameters. Does this means that Gromacs use
> the default parameter?
>

Yes, please do some tutorial material where the structure of the .top file
is explained (also in the reference manual from GROMACS). The early
structure sets up the parameters from databases that are part of GROMACS.


>      If we want to compare this topology with the topology from
> literature, where should I find these top parameters in Gromacs one by one?
>

share/gromacs/top/*.ff


>      Is these default parameter accurate enough to simulate polymer like
> Polyethelene or Polystyrene?
>

No idea. You should approach such questions by reading and understanding
the philosophy behind the force fields.

Mark


>      Thank you very much!
>
> Sincerely yours,
> Taisen Zuo
>
>  ;
> ; Ethanol, Jorgensen et al. JACS 118 pp. 11225 (1996)
> ;
> [ moleculetype ]
> ; name  nrexcl
> ETH     3
>
> [ atoms ]
> ;   nr    type   resnr  residu    atom    cgnr        charge          mass
>      1       opls_157       1     ETH       C       1   -0.18
>      2       opls_156       1     ETH       H       1   0.06
>      3       opls_156       1     ETH       H       1   0.06
>      4       opls_156       1     ETH       H       1   0.06
>      5       opls_157       1     ETH       C       2   0.145
>      6       opls_156       1     ETH       H       2   0.06
>      7       opls_156       1     ETH       H       2   0.06
>      8       opls_154       1     ETH      OA       2   -0.683
>      9       opls_155       1     ETH      HO       2   0.418
>
> [ bonds ]
> ;  ai    aj funct           c0           c1
>  1      5       1
>  3      1       1
>  4      1       1
>  2      1       1
>  7      5       1
>  6      5       1
>    8      5       1
>  9      8       1
>
>  [ pairs ]
>  ; i    j       func
>  2      6
>  2      7
>  2      8
>  3      6
>  3      7
>  3      8
>  4      6
>  4      7
>  4      8
>  1      9
>  6      9
>  7      9
> [ angles ]
> ;  ai    aj    ak funct           c0        c1
> ; H3
>  2      1       5       1
>  3      1       5       1
>  4      1       5       1
> ;
>  4      1       3       1
>  4      1       2       1
> ;
>  3      1       2       1
> ;
>  1      5       7       1
>  1      5       6       1
>  1      5       8       1
> ;
>  5      8       9       1
> ;
>  6      5       7       1
>  6      5       8       1
> ;
>  7      5       8       1
> ;
> [ dihedrals ]
>  2      1       5      6        3
>  3      1       5      6        3
>  4      1       5      6        3
>  2      1       5      7        3
>  3      1       5      7        3
>  4      1       5      7        3
>  2      1       5      8        3
>  3      1       5      8        3
>  4      1       5      8        3
>  1      5       8      9        3
>  6      5       8      9        3
>  7      5       8      9        3
>
>
> --
> Taisen Zuo
>
> China Spallation Neutron Source，Institute of High Energy Physics， Chinese
> Academy of Science
> A1-510, Zhongziyuan road NO.1, Dongguan, Guangdong, PR China. 523770
> Tel: 86-0769-89156495
> Cell: 13650469795
>
>
> 左太森
> 中科院高能物理研究所中国散裂中子源
> 广东省东莞市大朗镇中子源路1号A1-510
> 邮编：523770
> 办公电话：86-0769-89156495
> 手机：13650469795
> --
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