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
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
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
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
wrote:
> Hi Nikita,
>
> It's not like
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
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
Hi Nikita,
That's actually a good question, and I think it hasn't been phrased like
this before. I rephrase it slightly again, so it says "which parameters
should be considered part of a force field?"
The first thing that springs to mind is not really a parameter, but a vital
part of the force
Thank you sir for the reply...
a few queries are still there
1) what are the parameters that change according to force fields??
2) and what are the minimum cut offs for the parameters that changes
according to force fields or is there any link where the information can
be retrieved.
On 5/16/16 12:23 AM, Ms. Nikita Bora wrote:
Original Message
Subject: Re: simulation_time
From:"Ms. Nikita Bora"
Date:Mon, May 16, 2016 9:42 am
To: nik...@tezu.ernet.in
Original Message
Subject: Re: simulation_time
From:"Ms. Nikita Bora"
Date:Mon, May 16, 2016 9:42 am
To: nik...@tezu.ernet.in
--
On 5/14/16 2:25 AM, Ms. Nikita Bora wrote:
Respected Sir,
Recently i followed your tutorial for simulation of a 50 ns final mdrun of
protein-ligand complex where the value of rvdw=rcoulomb=1.4 was used. The
simulation runned at aorund 10 ns/day . While for the same complex when
Respected Sir,
Recently i followed your tutorial for simulation of a 50 ns final mdrun of
protein-ligand complex where the value of rvdw=rcoulomb=1.4 was used. The
simulation runned at aorund 10 ns/day . While for the same complex when
rvdw=rcoulomb=1 is made the run was 10 ns/day.
Sir i would
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