[gmx-users] Re: genbox Not enough memory

[Dr. Vitaly Chaban]

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
>