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 <[email protected]
<mailto:[email protected]>> 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
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ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
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ICTAS Doctoral Scholar
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Department of Biochemistry
Virginia Tech
Blacksburg, VA
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