Hi Martin,
I don't know if it's necessarily a memory leak -- there's no reason to me
why the memory should be getting freed in the first place based on the
commands you gave (in fact, I don't know if there even is a 'delete'
command). My suggestion would actually be to use the "reduce" program to
add hydrogens to the PDB files rather than using leap. Reduce is described
in the ambertools manual.
Hope this helps,
Jason
On Wed, Sep 29, 2010 at 9:34 AM, Martin Brieg <martin.brieg.kit.edu> wrote:
> Hello everyone,
>
> I am using tLeap to add hydrogens to heavy atom trajectories of MD
> simulations
> and large decoy sets. However i have noticed a very fast increase of memory
> usage of tleap when loading and saving alot of pdb files:
>
> the script for tleap looks like the following:
>
> source leaprc.ff03.r1
> pdb = loadPdb file1.pdb
> savePdb pdb file1.pdb
> pdb = loadPdb file2.pdb
> savePdb pdb file2.pdb
> pdb = loadPdb file3.pdb
> savePdb pdb file3.pdb
> ...
>
> The memory usage increases to 1 GB in about a minute or two and goes even
> further. Is this really a memory leak? Or is leap writing to some hidden
> variables that are not apparent from the input script and just need to be
> cleaned from time to time? If so, how do i do this?
>
> Regards
> Martin
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Sep 29 2010 - 07:00:06 PDT
