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
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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