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

[RAHUL SURESH]

Here i have added the report for the commands


Command line:
  *gmx editconf -f cu.gro -o cuNew.gro -bt cubic -d 1.0 -c*

Read 628 atoms
Volume: 579.929 nm^3, corresponds to roughly 260900 electrons
No velocities found
    system size :  3.716 91.693  1.702 (nm)
    diameter    : 91.698               (nm)
    center      : -0.048  0.153  0.001 (nm)
    box vectors :  3.715 91.693  1.702 (nm)
    box angles  :  90.00  90.00  90.00 (degrees)
    box volume  : 579.93               (nm^3)
    shift       : 46.897 46.696 46.848 (nm)
new center      : 46.849 46.849 46.849 (nm)
new box vectors : 93.698 93.698 93.698 (nm)
new box angles  :  90.00  90.00  90.00 (degrees)
new box volume  :822615.31               (nm^3)


Command line:
  *gmx solvate -cp cuNew.gro -cs spc216.gro -p cu.top -o solv.gro*

Reading solute configuration
GROup of MAchos and Cynical Suckers
Containing 628 atoms in 43 residues
Reading solvent configuration
216H2O,WATJP01,SPC216,SPC-MODEL,300K,BOX(M)=1.86206NM,WFVG,MAR. 1984
Containing 648 atoms in 216 residues

Initialising inter-atomic distances...

WARNING: Masses and atomic (Van der Waals) radii will be guessed
         based on residue and atom names, since they could not be
         definitively assigned from the information in your input
         files. These guessed numbers might deviate from the mass
         and radius of the atom type. Please check the output
         files if necessary.

NOTE: From version 5.0 gmx solvate uses the Van der Waals radii
from the source below. This means the results may be different
compared to previous GROMACS versions.

++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
A. Bondi
van der Waals Volumes and Radii
J. Phys. Chem. 68 (1964) pp. 441-451
-------- -------- --- Thank You --- -------- --------

Generating solvent configuration
Will generate new solvent configuration of 51x51x51 boxes
Solvent box contains 83316213 atoms in 27772071 residues

-------------------------------------------------------
Program:     gmx solvate, version 2016.4

Memory allocation failed:
std::bad_alloc

For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors


On Mon, Nov 27, 2017 at 11:53 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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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> Gromacs Users mailing list
>
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-- 
*Regards,*
*Rahul Suresh*
*Research Scholar*
*Bharathiar University*
*Coimbatore*