[gmx-users] simulation_time[Nikita Bora]

Justin Lemkul jalemkul at vt.edu
Thu May 26 13:46:10 CEST 2016 


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.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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-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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