# bad distribution of water molecules

Dear everyone

I am trying to simulate spc/e water flow through a channel with wall molecules in z direction. periodic boundary condition is applied in all directions. I set the wall temperature via nvt also nve ensemble is used for water molecules. but after few steps, the water molecules approach to the walls and a vacant space appears at the middle of the domain.
I was wandering what is the reason of wrong distribution of water molecules inside the domain.

I am using 14 Feb 2014 version.

regards,

Dear everyone

I am trying to simulate spc/e water flow through a channel with wall molecules in z direction. periodic boundary condition is applied in all directions. I set the wall temperature via nvt also nve ensemble is used for water molecules. but after few steps, the water molecules approach to the walls and a vacant space appears at the middle of the domain.
I was wandering what is the reason of wrong distribution of water molecules inside the domain.

I am using 14 Feb 2014 version.

regards,

Dear everyone

I am trying to simulate spc/e water flow through a channel with wall
molecules in z direction. periodic boundary condition is applied in all
directions. I set the wall temperature via nvt also nve ensemble is used for
water molecules. but after few steps, the water molecules approach to the
walls and a vacant space appears at the middle of the domain.
I was wandering what is the reason of wrong distribution of water molecules
inside the domain.

typos in the input?
errors in the input?

lots of possibilities. usually, the probability to mess something up
list larger than to get it right.

axel.

Dear Dr. Kohlmeyer, thanks for reply
i don’t know my setup is right for equilibrium or not. I checked the rest over and over.
here is the main part of equilibrium step in my input:

velocity spce create 288 1234 dist gaussian mom yes rot yes
fix 4 all nve

fix shakeh2o spce shake 1.0e-4 100 0 b 1 a 1
fix 2 lowwallatoms nvt temp 290.0 290.0 10
fix 3 topwallatoms nvt temp 290.0 290.0 10
fix 6 wallatoms spring/self \${spring}

do you think this gonna work to equilibrium the explained system?
Regards,

Dear everyone

I am trying to simulate spc/e water flow through a channel with wall
molecules in z direction. periodic boundary condition is applied in all
directions. I set the wall temperature via nvt also nve ensemble is used for
water molecules. but after few steps, the water molecules approach to the
walls and a vacant space appears at the middle of the domain.
I was wandering what is the reason of wrong distribution of water molecules
inside the domain.

typos in the input?
errors in the input?

lots of possibilities. usually, the probability to mess something up
list larger than to get it right.

axel.

Dear Dr. Kohlmeyer, thanks for reply
i don’t know my setup is right for equilibrium or not. I checked the rest over and over.
here is the main part of equilibrium step in my input:

velocity spce create 288 1234 dist gaussian mom yes rot yes
fix 4 all nve
fix shakeh2o spce shake 1.0e-4 100 0 b 1 a 1
fix 2 lowwallatoms nvt temp 290.0 290.0 10
fix 3 topwallatoms nvt temp 290.0 290.0 10
fix 6 wallatoms spring/self \${spring}

do you think this gonna work to equilibrium the explained system?

As has been explained here many, many times :
Nobody can say from only a few lines of input.

Errors can be everywhere and i don’t have a crystal ball…

If it’s a hydrophilic wall-water interaction, it might not be surprising to find the density of water overall should be higher than the liquid density. And since there’s no way in your system for the box size to change you have to lose molecules from somewhere…