On 10/21/12 8:21 AM, Ali Alizadeh wrote:
Dear Justin
It is true that we can not get profile volume vs. time(only nvt
step), but after that we performed production md, we can
illustrate profile density and volume profile vs. time. However we
cannot get constant volume!
Do I mistake? If it is possible , You can explain more about that fluctuation?
If the ensemble is NPT during the production run, then the box volume is not
constant. Pressure is constant (on average) and thus the box vectors will
fluctuate in response to the pressure coupling algorithm scaling the vectors.
If you are unclear on how this works, then please refer to the primary
literature for the pressure coupling algorithm you are using to understand what
it is doing.
-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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