[gmx-users] bonded parameter

[Mark Abraham]

Hi,

Either your topology doesn't use those parameters, or the interactions that
use them were converted to constraints by the settings in your .mdp file.

(By the way, it is better to talk about a "stage" of an MD workflow, as
"step" can be misunderstood to mean an integration step.)

Mark

‪On Wed, Aug 12, 2015 at 7:57 PM ‫حسن هاشم زاده‬‎ <
hashemzadehassan at gmail.com> wrote:‬

> but I delete bonded parameter from my force field in spite of this topology
> file was created  and all step is runing without any error
>
> 2015-08-12 21:56 GMT+04:30 Maryam Kowsar <maryam.kowsar at gmail.com>:
>
> > Hi Hassan,
> > For making a topology(.top) file all parameters of your forcefield is
> > needed.
> >
> > On Wed, Aug 12, 2015 at 9:37 PM, حسن هاشم زاده <
> hashemzadehassan at gmail.com
> > >
> > wrote:
> >
> > > Hi
> > >
> > > ?Which step of simulation the bonded parameters of available in a force
> > > field will be used
> > > --
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