On 5/26/16 7:16 AM, SAPNA BORAH wrote:
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
That's not a "slight" difference and can, in fact, undermine the entire
nonbonded setup. The net takeaway from this discussion (and all of the previous
ones on this topic) should be as follows:
1. The water model should be regarded as part of the force field; specific
applications (validated in the literature) may permit non-default selections.
2. The nonbonded setup is the most critical thing to get right; again, this is
not something that you can assume is going to make a small difference. It can,
in fact, ruin everything if not properly set up. We spend years of our lives
getting these force fields right, within certain operating parameters and
assumptions, only to have users assume they know better by trying to speed
things up (reducing cutoffs) or "be more accurate" (increasing cutoffs), neither
of which is legitimate.
3. Before touching anything, the user should investigate the chosen force field
- its origins, assumptions, previous applications, criticisms and revisions,
etc. that are published. If the user has not done this, how can he/she justify
that the force field should even be used? If you don't know the cutoffs, did
you go back and read about the force field, or are you trusting on blind faith
that existing hand-me-down protocols are correct, or that stuff you read in
tutorials/mailing lists/random Internet posts are actually scientifically valid?
There's a lot of homework that should be done before ever running a simulation,
and it's real science, not just some arbitrary set of numbers you can concoct.
You wouldn't walk into a chemistry lab and mix two clear liquids together
because they look pretty much the same, would you? ;)
-Justin
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.abra...@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 <sapnauser...@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 <tsje...@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" <nik...@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" <nik...@tezu.ernet.in>
Date: Mon, May 16, 2016 9:42 am
To: nik...@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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