[gmx-users] What is cth stand for, in the parameters file. It is not written in the latest manual 4.5.6.

[Mark Abraham]

On Fri, Nov 14, 2014 at 2:16 PM, Anik Sen <anik.sen at kemi.uu.se> wrote:

> What is cth stand for, in the parameters file. It is not written in the
> latest manual 4.5.6.


The angle function *is* documented, in table 5.5, like I said. The notation
is inconsistent between that table and the file you are using, but cth is
the force constant.


> Is kd the force constant for dihedral angles??
>

Yes. See table 5.5 for units.

Mark


>
>
> [ bondtypes ]
> ; i            j                func                 b0
>  kb
>  C          O                 1                 0.12300            502080.
>  C        OM                1                 0.12500            418400.
>
>
> ......
> [ angletypes ]
> ; i                   j                k                func
>   th0                cth
>  HO                OA            C                1
> 109.500            397.480
>  HO                OA           CH1             1                109.500
>            397.480
> ......
>
> [ dihedraltypes ]
> ;i              j              k              l              func
>         phase                  kd                  pn
> CA         CA           CA          OH              4
>  180.00                4.60240             2
>
> with regards
> Anik
>
>
> Dr. Anik Sen,
> Post Doctoral Fellow,
> Ångströmlaboratoriet- Uppsala Universitet
> Box 538
> SE-751 21 Uppsala
> Sweden
> Phone no:- +46-722781705
>
> ________________________________________
> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se [
> gromacs.org_gmx-users-bounces at maillist.sys.kth.se] on behalf of Mark
> Abraham [mark.j.abraham at gmail.com]
> Sent: 14 November 2014 12:44:02
> To: Discussion list for GROMACS users
> Subject: Re: [gmx-users] IMPORTANT
>
> Hi,
>
> Please use a descriptive subject. Your email is important to you, but that
> doesn't help anybody choose whether they might be able to help. :-)
>
> On Fri, Nov 14, 2014 at 12:30 PM, Anik Sen <anik.sen at kemi.uu.se> wrote:
>
> > Hei,
> >          I am using gromacs 4.5 version,
>
>
> Since you are doing new work, you should very likely be using a more recent
> version of Gromacs, to get faster performance and generally fewer bugs.
>
>
> > and i wanted to incorporate a file in the residue. its just a small
> > molecule, h2o2.
> > I had to change the four files in the amber03 forcefield which i was
> using.
> > atomtypes.atp, ffbonded.itp, ffnonbonded.itp and incorporate a file at
> the
> > .rtp.
> >
> > Now atomtypes and .rtp file was done with no problem.
> > For ffnonbonded, i had the sigma and epsilon and so it was done.
> > For ffbonded.itp;
> > in the bond types there is are two terms b0 and kb, which i have changed.
> > in the angle types thers is the theta as th0 and another term 'cth'. What
> > is this 'cth' and its unit.
> > For dihedral types what are kd and pn and there units?
> >
>
> See the appropriate tables in manual sections in chapter 5 and links
> therefrom; more recent Gromacs versions have better documentation here,
> too.
>
> Mark
>
> I want to know what these terms represent not the value.
> >
> > Thanking you
> > Anik
> >
> >
> >
> >
> >
> > *** STK-14 Uppsala *** https://sites.google.com/site/stkmuu14/
> > Dr. Anik Sen,
> > Post Doctoral Fellow,
> > Ångströmlaboratoriet- Uppsala Universitet
> > Box 538
> > SE-751 21 Uppsala
> > Sweden
> > Phone no:- +46-722781705
> > --
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