[gmx-users] High temperature Simulation
Justin A. Lemkul
jalemkul at vt.edu
Mon Oct 17 17:29:15 CEST 2011
Kavyashree M wrote:
> 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.
>
I would suggest investigating what an appropriate pressure value might be
(although I agree it's hard to say, and you may not be able to actually simulate
at such a pressure for stability reasons), equilibrate under NPT until the
pressure and temperature are stable, then switch to NVT to eliminate the boiling
issue. It is hard to say whether or not any force field or water model will
inherently be stable for these conditions, but high temperature MD is a topic
that is well-represented in the literature. I'd suggest you apply proven
methodology that makes sense in your case.
-Justin
> Thank you
> With Regards
> Kavya
>
> On Mon, Oct 17, 2011 at 8:45 PM, Justin A. Lemkul <jalemkul at vt.edu
> <mailto: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> <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 <http://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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--
========================================
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
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