[gmx-users] IMPORTANT

Mark Abraham mark.j.abraham at gmail.com
Fri Nov 14 12:44:06 CET 2014


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.


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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