[gmx-users] simulation_time[Nikita Bora]

[Mark Abraham]

Hi,

A report written by the people who designed the method that describes how
they used it *is* a direct way to know the values to use. People they often
publish with are also probably pretty reliable. Even better still are the
people who show why their parameter choices work. The models didn't arrive
by divine inspiration :-)

Mark

On Thu, May 26, 2016 at 8:42 AM SAPNA BORAH <sapnauser365 at gmail.com> wrote:

> hi...
> So there is no direct way to know the values to be used .
> however the last line is still unclear...
>
>
> Sapna Mayuri Borah
> c/o Dr. A. N. Jha
> Research student
> Tezpur University,
> India
>
> On Fri, May 20, 2016 at 12:00 PM, Tsjerk Wassenaar <tsjerkw at gmail.com>
> wrote:
>
> > 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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