On second thought, "remove" might do this. In any case, I still think
reduce is the way to go.
On Wed, Sep 29, 2010 at 9:44 AM, Jason Swails <jason.swails.gmail.com>wrote:
> 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
>>
>> _______________________________________________
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>> 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
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Wed Sep 29 2010 - 07:00:08 PDT
