Subject: Re: Re: [gmx-users] Gromacs 4 bug?

[Mark Abraham]

Bernhard Knapp wrote:
> Mark wrote:
> 
>> What's happening in the log files? What's the latest information in 
>> the checkpoint files? Could there be some issue with file system 
>> availability?
> 
> Hi Mark
> 
> Unfortunaltey I already deleted the simulation files which got stuck 
> after 847ps. But here is the output of another simulation done on the 
> same system but with an other pdb file. This one gets stuck after 179ps 
> with the following output:
> 
> The latest thing the checkpoint file says is:
> 
> "imb F  3% step 89700, will finish Wed Jul  1 09:11:00 2009
> imb F  3% step 89800, will finish Wed Jul  1 09:02:51 2009"

OK so there's no indication from GROMACS that it's experiencing trauma 
within the simulation. So now you need to try to restart close to the 
point you saw problems to see if the problem is reproducible. If it's 
not reproducible, then my guess, as last time, is that an NFS share is 
becoming unavailable, or some such. There are lots of other 
possibilities - a bug in GROMACS seems unlikely at this stage.

Mark