[gmx-users] system goes out of the water box

[Dallas B. Warren]

Belquis,

> everything seems fine and the MD run went smooth. However 
> when I look at the trajectory, I see that the drug goes of 
> the water box and the simulation ends up with the drug 
> attached to the outside of the box.
> 
> Does this mean that I should increase the size of my box? 
> before running the md, the drug was centered into the box of 
> water molecules.

Three letters or three words explain that and means everything is fine,
and recommend you read up on it either in the manual or any textbook
dealing with MD ...

PBC

Periodic Boundary Condition

Catch ya,

Dr. Dallas Warren
Lecturer
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 9524
---------------------------------
When the only tool you own is a hammer, every problem begins to resemble
a nail.