[gmx-users] Not enough memory. Failed to realloc

Justin Lemkul jalemkul at vt.edu
Mon Nov 27 19:23:26 CET 2017



On 11/27/17 11:26 AM, RAHUL SURESH wrote:
> Hi
>
>
>
> *gmx editconf -f cu.gro -o cuNew.gro -bt cubic -d 1.0 -c*

And how large is the resulting box? Are all the coordinates properly 
defined? What is the full screen output of gmx solvate up to the failure?

-Justin

> I have used the above command to generate the box. Infact I have used this
> command before and I never got any error.
>
> Thank you
>
> On Mon, Nov 27, 2017 at 7:07 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>> On 11/27/17 7:17 AM, RAHUL SURESH wrote:
>>
>>> Dear Users
>>>
>>> I am trying to carryout protein-metal interaction using charmm36 ff.
>>> During
>>> solvation *"gmx solvate -cp cuNew.gro -cs spc216.gro -p cu.top -o
>>> solv.gro"
>>> *i receive a error stating
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>> *"Fatal error:Not enough memory. Failed to realloc 3094482528 bytes for
>>> atoms_->atom,atoms_->atom=0(called from
>>> file/home/viji/Downloads/Gromacs/gromacs-2016.4/src/gromacs/
>>> topology/atomsbuilder.cpp,line
>>> 86)". *
>>> I have enough space to carry out this simulation and I am using 2016
>>> version of gromacs.
>>>
>> How large is your box? Are you sure you have set its size in nm, not A?
>>
>> -Justin
>>
>> --
>> ==================================================
>>
>> Justin A. Lemkul, Ph.D.
>> Assistant Professor
>> Virginia Tech Department of Biochemistry
>>
>> 303 Engel Hall
>> 340 West Campus Dr.
>> Blacksburg, VA 24061
>>
>> jalemkul at vt.edu | (540) 231-3129
>> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>>
>> ==================================================
>>
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>
>

-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==================================================



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