Scratch that comment about sparseness. I am short on sleep, and for a moment thought I was talking about constraints, not electrostatics.
On Fri, Mar 8, 2019 at 1:12 PM Sean Marks <sema...@seas.upenn.edu> wrote: > 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 > -- 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.