[gmx-developers] mdrun continuation

[Mark Abraham]

Emanuel Peter wrote:
> Dear developers,
> 
> At the moment I want to do a loop over several mdruns. For this purpose
> I included the function mdrunner after its first call in a for-loop.
> In this inner loop I have included gmx_hbond as a subroutine.
> The big problem is that there are problems with runtime-errors when I
> want to execute this mdrunner function more than just one time.
> I would like to check the H-bond statistics every mdrunner loop and I
> want to implement a prototype algorithm that probably could handle with
> this H-bond data.
> Did anyone of you ever treat a problem like this ?
> I know that there could be dangling pointers after the first call and
> this would lead to such runtime errors. I tried to solve this with the
> macro sfree.
> If anyone could give me some advice for this problem I would be very
> happy about that.
> What pointers do I have to delete?
> In what way should I try to clean my stack after a mdrunner call?

There has been a thread or two on this general issue in the last year or 
so. Last time, my advice was to question seriously whether you need to 
loop within mdrun, or might be better served looping within a script to 
call an iterate of mdrun. I can't tell from your description above why 
you might need to loop over mdrunner.

Mark