[gmx-users] High temperature Simulation

[Kavyashree M]

Ok, The protein I am going to simulate is from a hyperthermophilic organism
which lives in deep oceanic thermal vents. so in the deep vents the pressure
will be enormous. even though I do not have much information about the
magnitude of pressure in that site and inside the cell of that organism.. I
may
be able to get some rough estimate of pressure..

So I wanted to simulate this protein at a temperature near 90 or 100 deg C.

Thank you
With Regards
Kavya

On Mon, Oct 17, 2011 at 8:45 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> Kavyashree M wrote:
>
>> Hello,
>>
>> I am sorry those were two different questions..  I wanted to know what
>> this statement actually mean?
>> "The set pressure should reflect whatever system you are trying to model."
>>
>>
> You haven't fully explained what exactly you're trying to do yet, so I'm
> taking a stab in the dark.  Let's say you're trying to simulate a benchtop
> experiment with a protein in solution over a heating mantle at 350 K.  The
> pressure is 1 atm under such circumstances (NPT).  Now let's say you want to
> simulate the behavior of a protein solution in a bomb calorimeter (constant
> volume) at 350 K.  The pressure is not likely to be 1 atm under such
> circumstances (but then too, you'd use NVT instead of NPT, but maybe after
> NPT equilibration at whatever the necessary pressure is).  Without a fully
> detailed description of what you'd like to accomplish, I'm going to stop
> guessing.
>
> You've asked a lot of scattered questions about different topics, which
> makes it less efficient for people to help you and less clear for you to
> understand what we're trying to communicate back, even if it is somewhat
> generic.
>
> -Justin
>
>  Thank you
>> With Regards
>> Kavya
>>
>>
>>    I don't see the connection to my comment about pressure, but I'll
>>    address this anyway.  There is no temperature during EM.  Hence with
>>    "gen-vel = no" then no velocities are generated.  The settings for
>>    gen-temp and gen-seed are defaults that are assigned when none are
>>    provided in the input .mdp file.
>>
>>    I seem to recall that a pressure term is written during EM, but it
>>    is largely meaningless.
>>
>>    -Justin
>>
>>
>>    --     ==============================**__==========
>>
>>
>>    Justin A. Lemkul
>>    Ph.D. Candidate
>>    ICTAS Doctoral Scholar
>>    MILES-IGERT Trainee
>>    Department of Biochemistry
>>    Virginia Tech
>>    Blacksburg, VA
>>    jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>>    http://www.bevanlab.biochem.__**vt.edu/Pages/Personal/justin<http://vt.edu/Pages/Personal/justin>
>>    <http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>> >
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> --
> ==============================**==========
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
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