[gmx-users] interaction potential parameters and the forcefield.itp file

[Mark Abraham]

Hi,

Please see tables in chapter 5 of the manual.

Mark


On Sat, Jun 14, 2014 at 8:50 AM, akari karin <j.akarikarin at gmail.com> wrote:

> dear gromacs users,
> i am simulating carbon nanotubes. i am having some problems with my
> interaction potential in the forcefield.itp file.
> my forcefield.itp file looks like this-
>
> [ defaults ]
> ; nbfunc        comb-rule       gen-pairs       fudgeLJ fudgeQQ
> 1               3               yes             0.5     0.5
>
> [ atomtypes ]
> ; The charges here will be overwritten by those in the rtp file
> ; name       mass      charge    ptype      sigma      eps
>   CJ   6     12.01100     0.000       A    3.40000e-01  3.60000e-01 ;
>   HJ   1     1.00800      0.417        A    0            0         ;
>
> [ bondtypes ]
>
> ; i    j func        b0          kb
>   CJ    CJ      1    0.14000   478900.0   ; TRP,TYR,PHE
>   CJ    HJ      1    0.10800   307105.6   ; PHE, etc.
>
> [ angletypes ]
>   CJ     CJ     CJ      1   120.000    562.200   ; PHE(OL)
>   CJ     CJ     HJ      1   120.000    292.880   ;
>   HJ     CJ     HJ      1   117.000    292.880   ; wlj from HC-CM-HC
>
> [ dihedraltypes ]
>   CJ     CJ     CJ     CJ      3     30.33400   0.00000 -30.33400
> 0.00000   0.00000   0.00000 ; aromatic ring
>   HJ     CJ     CJ     HJ      3     30.33400   0.00000 -30.33400
> 0.00000   0.00000   0.00000 ; aromatic ring
>   HJ     CJ     CJ     CJ      3     30.33400   0.00000 -30.33400
> 0.00000   0.00000   0.00000 ; aromatic ring
>
>
>
> (i took it directly from chembytes)
>
>
> i have a few questions regarding this.
>
> 1. how should i input my torsion parameters? i saw in the manual that i
> should put it in the [ dihedraltypes ] but
> if i use functiontype of 3 i have 5 columns and i don't understand what
> each part means.
>
> 2.i could input my morse bond potentials (Kcr and rc) but could not find
> the place to input gamma. where should i put it?
>
> thanks in advance.
> --
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