Nilesh Dhumal wrote:
Hello Justin,
I used 0.1fs timestep and I could get dielectric constant around 56 which
looks ok. To get the dielectric constant around ~75, should I reduce the
timestep around 0.05fs.
I have no idea. Try it.
I used temperature 298k for my simulation and average tmep. I got is
297.83 K. I am doing NPT and used 1.0 bar as reference pressure in my
.mdp. I am getting average pressure around 2.58 bar.
I run the equilibration for 1ns.
Energy Average RMSD Fluct. Drift
Tot-Drift
-------------------------------------------------------------------------------
Temperature 297.83 10.9687 10.9643 -0.00165807
-1.07774
Pressure (bar) 2.57551 4246.51 4246.51 -0.0360116
-23.4075
Why there is change in pressure? Is there any wrong with simulation?
Not necessarily. Pressure fluctuates wildly, a fact that is stated on this list
weekly. You may want to try equilibrated with the Berendsen barostat (which I
find relaxes the system nicely), then move to a more correctly defined NPT
ensemble using Parrinello-Rahman. For systems that are far from equilibrium,
P-R allows for much larger fluctuations. You're also using a very small value
of tau_p (0.5); you should probably be using something on the order of 2.0 for
equilibration.
Also realize that you're looking at 2.57551 +/- 4246.51 and wondering if it's
statistically different from 1.0. You may find this post useful:
http://lists.gromacs.org/pipermail/gmx-users/2010-October/055403.html
-Justin
--
========================================
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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