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

[Anik Sen]

What is cth stand for, in the parameters file. It is not written in the latest manual 4.5.6. Is kd the force constant for dihedral angles??



[ 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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