[gmx-users] bonded parameter

[Mark Abraham]

Hi,

I mean that I can't possibly tell what your problem is, because you've
shared zero information. You probably want to look at the PDF reference
manual for the documentation of the "constraints" .mdp option. Whether that
matters depends what you've chosen, but I don't know that. See
http://www.gromacs.org/Support for clues on how you might succeed at
getting help from people.

Mark

On Wed, Aug 12, 2015 at 8:55 PM Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> 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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