[gmx-users] why my protein run out of the box?

Dallas B. Warren Dallas.Warren at vcp.monash.edu.au
Wed Mar 1 22:34:31 CET 2006

> I have a question. My system includes a small protein and some 
> water/ChCl3/Methanol solvents). Before I ran MD, I ran energy 
> minimization first. However, when I ran MD, the protein jumped out of 
> the solvent box after 3 ps and the simulation couldn't continue. Who 
> can tell me what happened? Thank you very much!

Might be an idea to provide more details.  Exactly what you did, what
the output from the various scripts were when the problem occurred etc.

What do you mean by "jumped out of the solvent box"?  Note, the box of
solvent will typically have PBC, so as a large molecule starts to
approach the edge of a box it appears to be outside the solvent, but it
isn't, it is sticking into the other side of the solvent box.

Catch ya,

Dr. Dallas Warren
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 9073
When the only tool you own is a hammer, every problem begins to resemble
a nail.

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