Hi Justin,
This is what I got from the log file: Initializing Domain Decomposition on 6 ranks Dynamic load balancing: auto Will sort the charge groups at every domain (re)decomposition Initial maximum inter charge-group distances: two-body bonded interactions: 4.882 nm, Bond, atoms 456 457 multi-body bonded interactions: 4.915 nm, Angle, atoms 457 459 Minimum cell size due to bonded interactions: 5.407 nm Scaling the initial minimum size with 1/0.8 (option -dds) = 1.25 Optimizing the DD grid for 6 cells with a minimum initial size of 6.758 nm The maximum allowed number of cells is: X 0 Y 0 Z 0 But when I check, this the atoms that is limiting (from .gro file) : 1MOL C1 455 0.728 1.339 1.541 1MOL C2 456 0.696 1.224 1.636 1MOL C3 457 0.737 1.220 1.769 1MOL C4 458 0.692 1.112 1.851 1MOL H4 459 0.713 1.112 1.951 And non of them tells me they are over 4nm, which I am not sure where else it could go wrong. The smallest length of my box is 2 nm and my cut-off length is 1 nm. Thank you for your help. By the way, do I reply to the gmx-u...@gromacs.org address or how do I reply without disturbing other users? Thank you again, Ben ________________________________ From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Justin Lemkul <jalem...@vt.edu> Sent: 08 July 2016 15:22 To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Problem with Group and Verlet cut -off scheme On 7/8/16 10:20 AM, Ben Tam wrote: > Hi Mark, > > > It shouldn't, what I am simulated is a crystal structure and my tabulated > forcefield is only up to 3nm. Do you think the problem is there? To avoid the > charge group, I am putting in the section of [atoms]: > > > [ atoms ] > ; nr type resnr residue atom cgnr charge mass typeB > chargeB massB > 1 Mg 1 MOL Mg 1 > 2 O1 1 MOL O1 2 > 3 O2 1 MOL O2 3 > 4 O3 1 MOL O3 4 > . . . . . . > > . . . . . . > > . . . . . . > > > ... etc. > > The DD setup section of the .log file will tell you exactly what the limiting interactions are. -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 [http://mackerell.umaryland.edu/~jalemkul/Images/lemkul_small.jpg]<http://mackerell.umaryland.edu/~jalemkul> Justin A. Lemkul - MacKerell Lab<http://mackerell.umaryland.edu/~jalemkul> mackerell.umaryland.edu Welcome to my site! To learn more about me and the work I am doing, please use the navigation links above. ================================================== -- 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. -- 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.