On 11/4/16 5:09 PM, Kevin Chen wrote:
Hi Gromacs Users, We 've observed some issues while creating huge simulation boxes (over35 nm* 35 nm * 35nm in size). Commands used for building our benchmarks showed as follow: gmx pdb2gmx -f 1AKI.pdb -o 1AKI_processed.gro -water spce gmx editconf -f 1AKI_processed.gro -o 1AKI_newbox.gro -c -box 33 33 33 -bt cubic gmx solvate -cp 1AKI_newbox.gro -cs spc216.gro -o 1AKI_solv.gro -p topol.top gmx grompp -f ions.mdp -c 1AKI_solv.gro -p topol.top -o ions.tpr gmx genion -s ions.tpr -o 1AKI_solv_ions.gro -p topol.top -pname NA -nname CL -nn 8 gmx grompp -f minim.mdp -c 1AKI_solv_ions.gro -p topol.top -o em.tpr The problem only showed up when using box size greater than 30nm * 30nm * 30 nm. Once the box is bigger than 30*30*30, the simulation always crashes during EM stage. However everything is fine when using any box sizes smaller than 30*30*30. As such, we are eager to know if that was something we did wrong or there's some sort of issues for Gromacs dealing with large systems. Any suggestions and pointers are welcome!
Crashes with what error? Are you simply running out of memory? -Justin -- ================================================== Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul ================================================== -- 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.
