[gmx-users] Re: genbox Not enough memory

[Justin Lemkul]

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 <vvchaban at 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.neale at 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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