[gmx-users] simulation_time[Nikita Bora]

[Tsjerk Wassenaar]

Hi Nikita,

It's not like there's a range to take a minimum from. It's this with this
force field and that with another. Any deviation will alter the behaviour
of the force field, and you'll have to show that the result is valid,
either by running tests, or by referring to a paper that has results from
such tests. The most suitable value is probably the one used by groups that
have direct ties to the developing group(s).


Hope it helps,


Tsjerk



On May 20, 2016 07:20, "Ms. Nikita Bora" <niki24 at tezu.ernet.in> wrote:

> Thanks Tsjerk
>
> That was really a good explanation. And it helped me out a lot.
> Still,I would like to know what are the standard values for these
> parameters as somewhere rvdw=1 and somewhere rvdw=1.4 is used.
>
> As earlier it was mentioned that with different force field different
> value is used so is there any link where i can get to know the minimum cut
> off values for these parameters and which value should be used for which
> force field or condition
>
> thanks
> Nikita
>
>
>
>  ---------------------------- Original Message ----------------------------
> > Subject: Re: simulation_time
> > From:    "Ms. Nikita Bora" <niki24 at tezu.ernet.in>
> > Date:    Mon, May 16, 2016 9:42 am
> > To:      niki24 at tezu.ernet.in
> >
> --------------------------------------------------------------------------
> >
> > Respected Sir,
> >
> > Thanks for the reply. I would further like to know that according to this
> > tutorial
> > (
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/07_equil2.html
> )
> > the rvdw=rcoulomb=1 is used for the protein while according to this
> > tutorial
> > (
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/07_equil2.html
> )
> > rvdw=rcoulomb=1.4 is used. why a different value for the simple protein
> > and protein-ligand complex is used??
> >
>
> Different force fields, different settings.
>
> -Justin
>
> >
>
>
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