[gmx-users] Re: Carbon nanotube force field
David van der Spoel
spoel at xray.bmc.uu.se
Mon Mar 5 18:55:03 CET 2007
m.alaghemandi at theo.chemie.tu-darmstadt.de wrote:
> Dear Prof. Dr. Van der Spoel,
> I'm simulating a system involving carbon nanotubes. As an initial test of
> my force field I want to simulate a single carbon nanotube. I've done
> simulations at constant volume and constant pressure. However, it seems
> that the energy is always too high and the tube wants to collapse on
> I used this Force Field:
> Morse potential (function 3 in GROMACS)
> D = 478.9 kJ/mol
> b_0 = 0.1418 nm
> beta = 21.867 nm^-1
> G96 angle (function 2 in GROMACS)
> theta_0 = 120.00
> fc = 562.2 kJ/mol
Is that the right one? Don't you want number 1
> Proper dihedral (function 1 in GROMACS)
> theta_max = 180.00
> fc = 12.06 kJ/mol
> mult = 2
> L-J (function 1 in GROMACS)
> c6 = 4*eps*sig^6 = 5.7353e-3 kJ nm^6/mol
> c12 = 4*eps*sig^12 = 1.8707e-5 kJ nm^12/mol
> Could you please tell me what is wrong?
Have you checked the periodicity?
How about the topology? Is it periodic?
Please put further questions on the mailing list.
> Mohammad Alaghemandi
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
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