[gmx-users] Re: genbox Not enough memory

[Juliette N.]

Hi,

I will try to compress before doing genbox. As for the number of atoms, as
I said I *dont *intend to fill up the whole box with solvent. So I put
around 4000 solvent molecules to get the desired polymer Wt%, hence there
would be a lot of free space for a total of 120 000 atoms approx..Also I
tried - cs solvent.gro but it stucks and doest work.

Thanks for the comments,
J.


On 10 October 2012 17:16, Dr. Vitaly Chaban <vvchaban at gmail.com> wrote:
> By the way, if you place your solvent molecule (-cs ____.gro) into a
> very large box, such as 10x10x10nm, genbox may perform well. I did NOT
> try, just an idea.
>
> For the overall system setup, I would rather follow the previous
> comments anyway.
>
>
>
> On Wed, Oct 10, 2012 at 10:49 PM, Dr. Vitaly Chaban <vvchaban at gmail.com>
wrote:
>> On Wed, Oct 10, 2012 at 10:24 PM, Juliette N. <joojoojooon at gmail.com>
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.
>>
>>
>> Sorry, I do not believe you. 120 000 atoms cannot ever fill the volume
>> of 250*250*250 nm^3.
>>
>>
>>> 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.?
>>
>> This "adding memory" is the appetit of the genbox in its current
>> incarnation. I am sure that the developers did not expect to apply
>> this utility for the systems larger than 30x30x30 nm. You can always
>> construct a very simple script that puts your solvent evenly
>> throughout the box.
>>
>> Why not to gently compress the box WITHOUT solvent..... Unless you
>> want to observe real-time folding of the polymer. It is probably not
>> so good idea to start with a huge box and super low density.
>>
>>
>> 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
>>
>>
>>
>>
>>
>>
>>> Thank you for your comments,
>>>
>>>
>>> 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
>>



-- 
Thanks,
J. N.