[gmx-users] simulation_time[Nikita Bora]

[SAPNA BORAH]

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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