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

[Mark Abraham]

As you can see in table 5.5, dihedraltype 3 is a Ryckaert-Belleman
dihedral, and there's a nice cross reference to the discussion of what the
five parameters mean. Your intended dihedral is of some other form, so
decide from chapter 4 what form makes most sense and look up how to do it
in table 5.5

Mark


On Sun, Jun 15, 2014 at 11:09 AM, akari karin <j.akarikarin at gmail.com>
wrote:

> 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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