[gmx-users] equilibrium for box of simulation
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.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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