[gmx-users] bonded parameter

[Mark Abraham]

Yes, but only you know which!

Mark

‪On Wed, Aug 12, 2015 at 8:45 PM ‫حسن هاشم زاده‬‎ <
hashemzadehassan at gmail.com> wrote:‬

>  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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