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

[akari karin]

thanks for your reply dr. mark.

i read the chapter you mentioned and solved the problem with gamma in the
morse bond potential.
but i could not find any suitable solution to the torsion parameters. how
can i input torsion parameters(k_c_phi and phi_c)?


On Sat, Jun 14, 2014 at 3:42 PM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> 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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