On 10/10/12 4:24 PM, Juliette N. wrote:
Hi again,
The reason I have this big box is that I have fully extended chains of
the length of ~ 250 nm,. In fact this 250 nm is the minimum size that
I can fit the chain in the box; and I am going to fill this box with
solvent and use NPT to increase the density. So I dont need to fill up
the box with solvent entirely. The total number of atoms would be
around 120 000.
I have access to a certain number of nodes. I am wondering if this
"adding of memory" is merely a hardware issue or there is some other
ways to get around this.?
Thank you for your comments,
This does not sound like a reliable protocol to me. I'm assuming that your
250-nm box is based on a completely linear polymer model, and you're hoping it
will collapse down under NPT conditions in the presence of some solvent?
The reason I (strongly) think this will fail is that you will have a large
amount of vacuum in your system, causing the box to rapidly shrink to conform to
the contents of the system. If the simulation doesn't completely crash (for a
variety of reasons), then you're going to likely end up with a polymer within a
long, rectangular box. That box will then violate the minimum image convention
if the polymer (still largely elongated) rotates even slightly.
genbox has a lot of memory leaks, some of which I believe are fixed for the
upcoming release (don't ask me when it will be out, I have no idea). The larger
the box, the worse the problems are.
-Justin
On 10 October 2012 13:14, Dr. Vitaly Chaban <vvcha...@gmail.com> wrote:
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
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========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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