[gmx-users] Re: genbox Not enough memory

[Dr. Vitaly Chaban]

On Thu, Oct 11, 2012 at 12:19 AM, Juliette N. <joojoojooon at gmail.com> wrote:
> 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.



If you do not fill the whole box, it would be probably essentially the
same as if you have no solvent at all.

If you initially compress your polymer in a vacuum, perhaps, you will
get better outcome with a smaller time-step and higher pressure.

Good luck!

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








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