[gmx-users] grompp is using a very large amount of memory on a modestly-sized system

[Sean Marks]

I understand now, thank you for the prompt response. While the matrix would
actually be quite sparse (since the constraints are localized to each ice
molecule), I take it that memory is being allocated for a dense matrix.

That aside, is it feasible to accomplish my stated goal of scaling
ice-water electrostatics while leaving other interactions unaffected? One
alternative I considered was manually scaling down the charges themselves,
but doing this causes the lattice to lose its form.

On Fri, Mar 8, 2019 at 12:28 PM Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 3/8/19 11:04 AM, Sean Marks wrote:
> > Hi, everyone,
> >
> > I am running into an issue where grompp is using a tremendous amount of
> > memory and crashing, even though my system is not especially large (63976
> > atoms).
> >
> > I am using GROMACS 2016.3.
> >
> > My system consists of liquid water (7,930 molecules) next to a block of
> ice
> > (8,094 molecules). The ice oxygens are restrained to their lattice
> position
> > with a harmonic potential with strength k = 4,000 kJ/mol/nm^2. I am using
> > the TIP4P/Ice model, which is a rigid 4-site model with a negative
> partial
> > charge located on a virtual site rather than the oxygen.
> >
> > My goal is to systematically reduce the electrostatic interactions
> between
> > the water molecules and the position-restrained ice, while leaving
> > water-water and ice-ice interactions unaffected.
> >
> > To accomplish this, I am modeling all of the ice molecules using a single
> > moleculetype so that I can take advantages of GROMACS' FEP features to
> > selectively scale interactions. I explicitly specify all constraints and
> > exclusions in the topology file. This moleculetype contains one virtual
> > site, 3 constraints, and 4 exclusions per "residue" (ice molecule).
> >
> > When I run grompp, I receive the following error, which I think means
> that
> > a huge block of memory (~9 GB) was requested but could not be allocated:
> >
> > =====
> > Command line:
> >    gmx grompp -f npt.mdp -c md.gro -p topol.top -n index.ndx -r
> > initconf_packmol.gro -o input.tpr -maxwarn 2 -pp processed.top
> >
> > ...
> >
> > Generated 21 of the 21 non-bonded parameter combinations
> > Generating 1-4 interactions: fudge = 0.5
> > Generated 21 of the 21 1-4 parameter combinations
> > Excluding 3 bonded neighbours molecule type 'ICE'
> > turning H bonds into constraints...
> > Excluding 3 bonded neighbours molecule type 'SOL'
> > turning H bonds into constraints...
> > Coupling 1 copies of molecule type 'ICE'
> > Setting gen_seed to 1021640799
> > Velocities were taken from a Maxwell distribution at 273 K
> > Cleaning up constraints and constant bonded interactions with virtual
> sites
> > Removing all charge groups because cutoff-scheme=Verlet
> >
> > -------------------------------------------------------
> > Program:     gmx grompp, version 2016.3
> > Source file: src/gromacs/utility/smalloc.cpp (line 226)
> >
> > Fatal error:
> > Not enough memory. Failed to realloc -8589934588 bytes for il->iatoms,
> > il->iatoms=25e55010
> > (called from file
> >
> /home/semarks/source/gromacs/2016.3/icc/serial/gromacs-2016.3/src/gromacs/
> > gmxpreprocess/convparm.cpp,
> > line 565)
> >
> > For more information and tips for troubleshooting, please check the
> GROMACS
> > website at http://www.gromacs.org/Documentation/Errors
> > -------------------------------------------------------
> > =======
> >
> > In the hope that it helps with diagnosing the problem, here is my mdp
> file:
>
> The problem is this:
> > couple-intramol = no    ; don't adjust ice-ice interactions
> >
> This setting causes the creation of a large exclusion matrix, which in
> your case is approximately 32,376 x 32,376 elements. For small
> molecules, this generally isn't an issue, but since you're trying to
> modulate a large number of molecules within a much larger
> [moleculetype], the memory requirement goes up exponentially.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Office: 301 Fralin Hall
> Lab: 303 Engel Hall
>
> Virginia Tech Department of Biochemistry
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalemkul at vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==================================================
>
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-- 
Sean M. Marks
PhD Candidate
Dept. of Chemical and Biomolecular Engineering
University of Pennsylvania
SeanMarks1123 at gmail.com