> When I want to analyze hydrogen binds of a 30-mer DNA with ptraj I got the
> following error:
>
> ERROR in safe_malloc: Error in alloc of -2030981184 bytes
Yes, this means you are asking for more memory than your system has
available... A clue comes from the output:
> 7> HBOND saved to series hbt,
> data will be sorted, intra-residue interactions will NOT be included,
> Distance cutoff is 3.00 angstroms, angle cutoff is 120.00 degrees
> Hydrogen bond information will be dumped for occupancies > 0.05
> Estimated memory usage for this hbond call: 42.41 GB
> donors: 953 acceptors: 3974 frames: 1000
Estimated memory usage: 42 GB.
It is unlikely your machine has 42 GB of RAM.
The memory usage scales as something like donors*acceptors, so try first
to do the analysis in two runs, with half of the acceptors chosen in one
run, and half in the second. If this still blows memory, break it up
further.
3 angstroms is a fairly tight h-bond; I would recommend something closer
to 3.5 A.
> 7> HBOND saved to series time, output to file hb3_135,
> data will not be sorted, intra-residue interactions will NOT be included,
> Distance cutoff is 3.00 angstroms, angle cutoff is 135.00 degrees
> Hydrogen bond information will be dumped for occupancies > 0.00
> Estimated memory usage for this hbond call: 42.40 GB
> donors: 953 acceptors: 3974 frames: 1000
>
> 7> HBOND saved to series time, output to file hb3_120,
> data will not be sorted, intra-residue interactions will NOT be included,
> Distance cutoff is 3.00 angstroms, angle cutoff is 120.00 degrees
> Hydrogen bond information will be dumped for occupancies > 0.00
> Estimated memory usage for this hbond call: 42.40 GB
> donors: 953 acceptors: 3974 frames: 1000
>
> 7> HBOND saved to series time, output to file hb3.5_120,
> data will not be sorted, intra-residue interactions will NOT be included,
> Distance cutoff is 3.50 angstroms, angle cutoff is 120.00 degrees
> Hydrogen bond information will be dumped for occupancies > 0.00
> Estimated memory usage for this hbond call: 42.40 GB
> donors: 953 acceptors: 3974 frames: 1000
>
> 7> HBOND saved to series time, output to file hb3.5_135,
> data will not be sorted, intra-residue interactions will NOT be included,
> Distance cutoff is 3.50 angstroms, angle cutoff is 135.00 degrees
> Hydrogen bond information will be dumped for occupancies > 0.00
> Estimated memory usage for this hbond call: 42.40 GB
> donors: 953 acceptors: 3974 frames: 1000
You certainly do not likely have a machine with 42*5 GB of RAM, unless you
have some serious cash or access to a larger shared memory machine (like
an SGI). Break the hbond runs into separate and smaller runs.
--tec3
> MemTotal: 5054332 kB
> SwapTotal: 32764556 kB
p.s. you have only 5 GB of physical RAM available for the analysis, ~30 GB
or so if you're willing to thrash swap... I would recommend breaking the
hbond analysis into separate runs for each hbond call and also to break
the list of acceptors into more than two pieces. Are you really sure you
want information on that entire set of 953 donors and 3974 acceptors?
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Received on Sat Sep 04 2010 - 14:00:03 PDT
