[gmx-users] Not enough memory. Failed to realloc
Justin Lemkul
jalemkul at vt.edu
Tue Nov 28 14:40:43 CET 2017
On 11/27/17 11:55 PM, RAHUL SURESH wrote:
> Dear Justin
>
> It worked. Actually by its own. I reconstructed the pdb and gave again.
For the sake of completeness, the original problem was indeed due to a
massive box size, which was probably just incorrectly set. You had a
92-nm y-box vector and as a result, solvate was trying to add nearly 28
million(!) water molecules. This would definitely exhaust memory on
nearly any common computer.
-Justin
> Thank you so much for your time
>
> On Tue, Nov 28, 2017 at 10:08 AM, RAHUL SURESH <drrahulsuresh at gmail.com>
> wrote:
>
>> This error occur only for this particular pdb structure. The protein here
>> is attached with a metal ion. The necessary changes are made to the
>> charmm36 ff.
>>
>> Should be some error in my pdb?
>>
>> On Tue, Nov 28, 2017 at 10:04 AM, RAHUL SURESH <drrahulsuresh at gmail.com>
>> wrote:
>>
>>> 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
>>>>>>
>>>>>> ==================================================
>>>>>>
>>>>>> --
>>>>>> Gromacs Users mailing list
>>>>>>
>>>>>> * Please search the archive at http://www.gromacs.org/Support
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>>>>>>
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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
>>>>
>>>> ==================================================
>>>>
>>>> --
>>>> Gromacs Users mailing list
>>>>
>>>> * Please search the archive at http://www.gromacs.org/Support
>>>> /Mailing_Lists/GMX-Users_List before posting!
>>>>
>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>>
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>>>>
>>>
>>>
>>> --
>>> *Regards,*
>>> *Rahul Suresh*
>>> *Research Scholar*
>>> *Bharathiar University*
>>> *Coimbatore*
>>>
>>
>>
>> --
>> *Regards,*
>> *Rahul Suresh*
>> *Research Scholar*
>> *Bharathiar University*
>> *Coimbatore*
>>
>
>
--
==================================================
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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