[gmx-users] Strange pressure coupling behaviour, rapid expanding box

Kamps, M. m.kamps at student.rug.nl
Fri Dec 23 12:41:02 CET 2016

Dear Justin,

Thanks for your reply! I have tried the simulation again but this time
with opls_140, which is the same Hydrogen atom as is being used in the
polymer. This does use small values for sigma and epsilon. However
this made no difference, the box behaved the same.

Since I'm using semiisotropic coupling, and use different values for
the xy and z compressibility, I tried altering these values. In the
current situation the xy compressibility is derived from the
isothermal compressibility of gold, which is 5.77e-7. For the z
compressibility, I used 4.5e-5, which is the compressibility of water.
My thoughts were that maybe the surface caused a lot of pressure on
the system, therefore I greatly increased the compressibility in the
xy direction, to the point is higher than that of water (5.77e-4), and
I've decreased the compressibility in the z direction to 4.5e-6. This
only caused the system to expand less rapidly, but still only expand
in the z direction. The surface atoms (placed in their optimal
position), perfectly maintain the xy box.

I'm really unsure on what is causing this error, are there any other ideas?

Also, what happens when you set nwall=1? If there is no wall there,
the atoms can pass through the upper z plane, with just as the other
periodic planes, however, where do these atoms come back to? Since the
bottom plane is defined as a wall? How does this work? I can't find
this answer in the manual.


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