ps: There is a fix for this issue in Gerrit code review:
https://gerrit.gromacs.org/#/c/1175/
which introduces a fix genbox -allpair. This avoid the memory-leaky
neighbor searching, which is the reason for your problem.
Jochen
Am 10/11/12 10:56 AM, schrieb Jochen Hub:
Hi,
this is due to the way genbox -ci is currently implemented. It calles
add_conf() too often which leaks memory. So you'll have to edit the code.
Jochen
You'll have to edit the genbox code in order
Am 10/10/12 7:14 PM, schrieb Dr. Vitaly Chaban:
Thanks..You are right...The last line of gro file says 250 so it is
in nm!...
On 10 October 2012 12:30, Christopher Neale
<chris.ne...@mail.utoronto.ca> wrote:
Sounds like you ran out of memory. Many clusters have a few
large-memory nodes. Can you use one of those?
It's failing on a call for 1.3 Gb of memory, which by itself isn't
really a lot...
Also, can you confirm 250 A box length, not 250 nm box length?
Gromacs defines length in units of nm.
Chris.
-- original message --
I am trying to build a polymer in solvent system by solvating my fully
extended polymer chains in a box of size 250 250 250 A. I am adding
4500 solvent molecules as below
genbox -cp Solute.gro -ci solvent.gro -o solvated.gro -nmol 4500
Adding solvents is a slow process and takes much time and at the end
I get:
Program genbox, VERSION 4.5.4
Source code file: smalloc.c, line: 214
Fatal error:
Not enough memory. Failed to realloc 1338273212 bytes for grid->nra,
grid->nra=0x0
(called from file nsgrid.c, line 483)
For more information and tips for troubleshooting, please check the
GROMACS
website at http://www.gromacs.org/Documentation/Errors
Is this happening because of the huge amount of free space to be
filled with the solvent? Please help me.
Genbox sometimes suffers from the out-of-memory error. Based on my own
investigation, this is indeed what happens here, because the utility
uses a kind of grid during its operation. The larger the cell, the
more hungry it becomes, no matter how many molecules you want to
insert. The standard advice therefore applies - add memory...
Another question is why you need such a huge box? The only thing I
could imaging is simulating a droplet-vapor/air interface...
Another advice is to start with a smaller box and then extend its
deminsions using editconf (which does not "care about the box size").
Dr. Vitaly V. Chaban
MEMPHYS - Center for Biomembrane Physics
Department of Physics, Chemistry and Pharmacy
University of Southern Denmark
Campusvej 55, 5230 Odense M, Denmark
--
---------------------------------------------------
Dr. Jochen Hub
Computational Molecular Biophysics Group
Institute for Microbiology and Genetics
Georg-August-University of Göttingen
Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany.
Phone: +49-551-39-14189
http://cmb.bio.uni-goettingen.de/
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