[gmx-users] box size criterion in high temperature and constant pressure

Dallas Warren dallas.warren at vcp.monash.edu.au
Wed Jan 28 22:19:01 CET 2004

>At first, The peptide size detrmine the box size (in initialization).
>in high temperature(350-400K) and constant pressure, Are there other 
>for box size?

What sort of electrostatics that you use, eg if cut-offs then box side 
lengths have to be > 2 times the cut-off, otherwise each atom will see 
themselves through the periodic boundary condition.

The amount of water (distance) required around the peptide to ensure that 
it doesn't interact with itself through the periodic boundary condition or 
cause unrealistic behaviour.  I don't work with large molecules, but have 
found that even with small ones if the box is too small you can cause 
ordering/phase artefacts quite easily.

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
When the only tool you own is a hammer, every problem begins to resemble a nail.

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