[gmx-users] Not enough memory. Failed to realloc
RAHUL SURESH
drrahulsuresh at gmail.com
Tue Nov 28 18:42:48 CET 2017
Hi
Yeah. I understood that.. thanks a lot for your patience
On Tue, 28 Nov 2017 at 7:10 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
> 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
> >>>>>> /Mailing_Lists/GMX-Users_List before posting!
> >>>>>>
> >>>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >>>>>>
> >>>>>> * For (un)subscribe requests visit
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> or
> >>>>>> send a mail to gmx-users-request at gromacs.org.
> >>>>>>
> >>>>>>
> >>>>>
> >>>> --
> >>>> ==================================================
> >>>>
> >>>> 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
> >>>>
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> >>>> /Mailing_Lists/GMX-Users_List before posting!
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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
>
> ==================================================
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at
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> posting!
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>
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>
--
*Regards,*
*Rahul Suresh*
*Research Scholar*
*Bharathiar University*
*Coimbatore*
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