On 7/16/14, 3:43 AM, Timothy Click wrote:
Thanks for the reply and the helpful suggestion, Justin. I have now used g_x2top, changed the necessary parameters to match the CHARMM36 cgenff (graphene carbon as CG2R61). When I run a minimization with the graphene sheet defined as a freeze group, I receive the following error:
What was your exact g_x2top command?
WARNING: Listed nonbonded interaction between particles 6 and 48 at distance 3f which is larger than the table limit 3f nm. This is likely either a 1,4 interaction, or a listed interaction inside a smaller molecule you are decoupling during a free energy calculation. Since interactions at distances beyond the table cannot be computed, they are skipped until they are inside the table limit again. You will only see this message once, even if it occurs for several interactions. This, of course, leads me to believe that I have an issue with the [ pairs ] section of the topology file created by g_x2top. The pairs are defined with a function of 1.
The fact that a pair interaction is failing is not indicative of pairs being wrong, merely that the forces those atoms are experiencing are causing them to badly distort.
My system topology file looks like this: ; Include forcefield parameters #include "charmm36.ff/forcefield.itp" #include "/home/tclick/research/gra/gra.itp" #include "/home/tclick/research/bglc/top/glucan.itp" #include "/home/tclick/research/dma/single/dma.itp" ; Include chain topologies ;#include "topol_Other.itp" ;#include "topol_Other2.itp" [ system ] ; Name Sugar between grapehene bilyaer [ molecules ] ; Compound #mols Graphene 2 Glucan 1 DMA 6005 #ifdef POSRES #include "posre_gra.itp" #include "posre_bglc.itp" #endif
This #ifdef block will have no effect, as it comes after the system-level directives.
-Justin -- ================================================== Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 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.
