Hi, I don't have a solution for the question at hand, but it'd be great to have your inputs attached to a new issue at https://redmine.gromacs.org, so that we can have such an input case to test with, so that we can improve the simplistic implementation! Please upload it if you can.
Mark On Fri., 8 Mar. 2019, 19:24 Sean Marks, <sema...@seas.upenn.edu> wrote: > 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? 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