[gmx-users] bonded parameter

[حسن هاشم زاده]

 this means that "bonded parameter" not necessary for my work or that my
work is wrong

2015-08-12 22:53 GMT+04:30 Mark Abraham <mark.j.abraham at gmail.com>:

> 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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