[gmx-users] High temperature Simulation

[Justin A. Lemkul]

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://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

========================================