[gmx-users] simulation_time[Nikita Bora]

[SAPNA BORAH]

That seems quite clear nw.. thanks.. :)
so a slight deviation from values rvdw=1.4 to rvdw=1 and r coulomb=1.4 to r
coulomb=1
wont matter much unless its experimentally validated

Sapna Mayuri Borah
c/o Dr. A. N. Jha
Research student
Tezpur University,
India

On Thu, May 26, 2016 at 1:59 PM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> 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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