[gmx-users] How to run NPT (anisotropic simulatio) for urea-water system with variable axis only in z direction

[Mark Abraham]

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