Re: targeted molecular dynamics

From: sakthi kumaran (persakthi_at_gmail.com)
Date: Thu Mar 17 2011 - 09:08:25 CDT

Dear all
    according to my understanding, the parameter file I am using for
describing the quantiites of force field parameters as here,,,,,

BONDS
!V(bond) = Kb(b - b0)**2
!
!atom type Kb b0
C C 305.000 1.3750

ANGLES
!V(angle) = Ktheta(Theta - Theta0)**2
!V(Urey-Bradley) = Kub(S - S0)**2
!
!atom types Ktheta Theta0 Kub S0
C C C 40.000 120.00 35.00 2.41620

DIHEDRALS
!V(dihedral) = Kchi(1 + cos(n(chi) - delta))
!
!atom types Kchi n delta
C C C C 3.1000 2 180.00

NONBONDED nbxmod 5 atom cdiel shift vatom vdistance vswitch -
cutnb 14.0 ctofnb 12.0 ctonnb 10.0 eps 1.0 e14fac 1.0 wmin 1.5
!V(Lennard-Jones) = Eps,i,j[(Rmin,i,j/ri,j)**12 - 2(Rmin,i,j/ri,j)**6]
!
!atom ignored epsilon Rmin/2
C 0.000000 -0.070000 1.992400

END

whether this parameter file is correct. I intend to find the interaction
potential energy minima between the two capped nanotubes(considered only the
edge 120 atoms of each side). please help me in justifying this parameter
file so that I could correct myselff

How to exactly create one's own customized parameter file for use in
simulation with namd

thank you,

cheers
Sakthi

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