[gmx-users] Gromacs and graphene sheets

Timothy Click tclick at nctu.edu.tw
Wed Jul 16 09:44:18 CEST 2014

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:

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.

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"


柯明 Timothy H. Click, Ph.D.
Department of Biological Science and Technology
Institute of Bioinformatics and Systems Biology
National Chiao Tung University
208 Lab Building 1, 75 Bo-Ai St.
Dong District, Hsinchu, Taiwan 30062
tclick at nctu.edu.tw

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