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 <jalem...@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 > > jalem...@vt.edu | (540) 231-3129 > http://www.thelemkullab.com > > ================================================== > > -- > 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 > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Sean M. Marks PhD Candidate Dept. of Chemical and Biomolecular Engineering University of Pennsylvania seanmarks1...@gmail.com -- 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 https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.