[gmx-users] Gromacs and graphene sheets

[Dr. Timothy Click]

Greetings from Taiwan. I am attempting to simulate a sugar with a graphene sheet in Gromacs 4.6.5. I made the grapheme sheet using VMD, which does not number the carbons according a bond order. However, Gromacs seems to expect this (e.g., 1 bonded to 2, not 1 bonded to 15). I realize that I will have the grapheme sheet as fixed atoms, but this configuration seems to toy with the energies. I have even tried to use pdb2gmx with a PDB that had CONECT statements without success. I am using Gromacs 4.6.5, the Charmm 36 force field, water, and ions. A simple minimization without constraints causing the grapheme sheet to become unbounded and begin with ugh energies (10E8 kJ/mol).

I have thought about switching to Gromacs 5.0, but I don't know whether this problem could be solved by the switch. Any suggestions will be appreciated.
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Cordially,
柯明 Timothy H. Click, Ph.D.
Department of Biological Science and Technology
National Chiao Tung University
Rm. 208, Lab Building I, 75 Bo'Ai Street, Dong District
Hsinchu City, Taiwan 300 (R.O.C.)
tclick at nctu.edu.tw