[gmx-users] Reg; MD of DCE part II

Dallas Warren Dallas.Warren at monash.edu
Tue Oct 26 02:03:48 CEST 2010

>I performed md simulation of 108 dichloroethane molecules in
isothermal-isobaric ensemble with the box size

>3.002*2.17*2.17. after the simulation my box size has changed
considerably from the initial size to 2.87882 2.08095

>2.08095.why this happens?


Density was obviously too lower under the conditions of the simulation.
Look at the change of pressure, volume and density for the box during
that simulation.


>my second question is can i have a control over the box dimensions
changes during md (i.e when the box dimensions

>changes during md i want to change it only on one axis(say x axis) and
want to keep the length of the other two axis (say

>y and z) same as that of my initial box size? any help is highly


Look at the pressure coupling settings, look at anisotropic pressure


Catch ya,

Dr. Dallas Warren

Medicinal Chemistry and Drug Action

Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.warren at monash.edu

+61 3 9903 9304
When the only tool you own is a hammer, every problem begins to resemble
a nail. 



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