[gmx-users] more than 2 step*.pdb files?

Tsjerk Wassenaar t.a.wassenaar at chem.rug.nl
Wed Jun 4 11:46:01 CEST 2003

Hmm, come to think of it, it occured to me too, though with two 
step*.pdb files, but also two #step*.pdb# files. It didn't really strike 
me, and was not much of a problem, running only on two processors.

The system in my case is also a receptor in a bilayer in water. If you 
want more details, just mention.

Groetjes ;)


Anton Feenstra wrote:

> Hi All,
> My run of protein, ligand and water crashed, leaving three step*.pdb
> files, in stead of the two (crash and pre-crash) that I expect. What
> is more, there are three backup files (#step*.pdb.[12]#), one for one
> of the step*.pdb and two for another. I'm running on 6 CPU's, so it
> seems it is connected to the paralellism, maybe all CPU's think it
> is their job to write the files? If so, they should be marked by CPU
> #, so they don't overwrite each other.
> Anyone had this before?
> A coleague of mine had encountered this error before, but now I see it
> myself also (for the first time). His system is a bilayer, receptor and
> water and he gets many step*.pdb files (tens, or more). I'm not sure
> how many CPU's he uses. In his case, this has resulted in a full disk
> at least once, so there is a problem.

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