[gmx-users] Re: Carbon nanotube force field

[David van der Spoel]

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
> itself.
> I used this Force Field:
> 
>  Bonds:
>  Morse potential (function 3 in GROMACS)
>  D = 478.9 kJ/mol
>  b_0 = 0.1418 nm
>  beta = 21.867 nm^-1
> 
>  Angles:
>  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
> 
> 
>  Dihedrals:
>  Proper dihedral (function 1 in GROMACS)
>  theta_max = 180.00
>  fc = 12.06 kJ/mol
>  mult = 2
> 
>  Pairs:
>  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.

> 
> Regards,
> 
> Mohammad Alaghemandi
> 
> 


-- 
David.
________________________________________________________________________
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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