[gmx-users] change in box-size

[Dallas Warren]

Derrick,

>i was just curious if someone could put my mind at ease at something
>that has only dawned on me recently, i am running 1ns simulation with a
>DPPC monolayer and water and while i ran energy minimization, the system
>size remained unchanged but after i ran it with integrator = md, the
>system size changed from a 60x60x60 box to about 47x47x47 box. is this
>normal? thank you in advance.

During the em stage, was their any pressure coupling employed?  If not, 
then the box size isn't going to change.  When you then do the md stage, 
pressure coupling appears to have been used and the box size adjusts 
accordingly.  Check your pressure and density of the system to make sure it 
is doing what it should.

Catch ya,

Dr. Dallas Warren
Research Fellow
Department of Pharmaceutical Biology and Pharmacology
Victorian College of Pharmacy, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.warren at vcp.monash.edu.au
+61 3 9903 9083
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