[gmx-users] equilibrium for box of simulation

Justin Lemkul jalemkul at vt.edu
Thu Oct 4 16:22:54 CEST 2012

On 10/4/12 10:06 AM, mohammad agha wrote:
> Dear GROMACS Users,
> I asked this question before but I don't understand it!
> I placed several materials in my box of simulation for example box with 6nm*6nm*6nm and my materials are not placed in the smaller box but when I equilibrate my system, the box became smaller and temperature and pressure also equilibrate. my question is: is my system and equilibrate mistake, because of reach to smaller box? Is there equilibriums with reach to smaller box?

What do you mean by "my materials are not placed in the smaller box"?

If a box compresses, it is because the initial configuration was incompatible 
with the desired equilibration conditions and it contracted produce the desired 
quantity (likely pressure).



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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