Sivashangari Gnanasambandam wrote:
Hi,
I am trying to study the dissolution of urea in water. After adding the
water molecule using genbox, I did the energy minimization by applying
pbc. Then I run the equilibration for 300ps using NPT anisotropic
pressure coulpling and variable axis only in the z direction. The
reference pressure is 1 bar. After the run, the cystal structure is
deformed (which should n't be).
So, reading between the lines, you have a crystal of urea surrounded by
a water bath? Please spell these things out. How big is the crystal, how
much water did you add...
I would suggest equilibrating with NVT first to get the temperature
reasonable, and then (using gen_vel = no to keep the velocities) relax
to NPT. I would also study the system with isotropic pressure coupling
initially, on the usual "learn to walk before learning to run" theory.
How close is the initial density to the real density?
The mdlog file shows the avg pressure in the range of 2-4e+2 bar.
What is the average of 10000, 5000, 100, 4,2,-2, and 3? You can't get a
sensible average by looking at the whole of an equilibration run. Use
g_energy -W to look at plots with xmgrace, and then -b and -e to take
sensible subsets of the simulation period.
Mark
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