Amit Choubey wrote:
Hi Justin,
Since the density (1 gm/cc) and T (300 K) correspond to ambient
condition, should not the equation of state dictate a pressure around 1 atm?
If the equation of state involves temperature and pressure, yes. Sounds like
you want to be using an NPT ensemble, not NVE. For NVE, your volume and energy
are conserved, so there should (in theory) be little deviation from whatever
your starting conditions are.
-Justin
thank you
amit
On Sun, May 16, 2010 at 2:07 PM, Justin A. Lemkul <jalem...@vt.edu
<mailto:jalem...@vt.edu>> wrote:
Amit Choubey wrote:
Hi Everyone,
I was doing MD with SPC waters and found something which i am
not sure how to explain.
I made a box of SPC water of dimension 4x4x4 nm^3 and filled
with water using grenbox .
I then did a nvt simulation at 300 K for 1 ns . I used berendsen
coupling and Reaction - Field for coulomb interaction. Cut off
were all set to 1 nm. Temperature did converge to 300 K. After
this i turned of nvt and did nve with RF-zero for another ns.
Energy was well converged during this (RMSD < 0.1 %).
Temperature was also around 304 K (RMSD < 1%). But the pressure
was 1.1 Kilobar with a fluctuation of 20 % . I don understand
this, shouldnt this be around 1 bar ? Could some one suggest
whats on ?
Since an NVE ensemble employs neither a thermostat nor a barostat, I
don't know why you'd expect that.
-Justin
Thank you,
amit
--
========================================
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
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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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