From: Kiarash Hosseini (kiarash.hosseini_at_gmail.com)
Date: Tue Apr 10 2012 - 04:24:10 CDT
*Dear all;*
*Good time.*
*
*
*I have created a model containing a **(3,6) **CNT and two gold electrodes,
solvated in H2S gas. The PSF of the same has been created by VEGA ZZ
software.*
*In case of running I encounter an error "DIDN'T FIND vdW PARAMETER FOR
ATOM TYPE AUC". in which AUC is the atom type, I have created for Gold
Crystal.*
*The parameters below have been added to the existing Parameter File in
NAMD tutorial files (**par_all27_prot_lipid.inp)**:*
*
BONDS
!
SH2S HH2S 275.000 1.34
AUC AUC 0.000 0.00
*
*
ANGLES
!
!V(angle) = Ktheta(Theta - Theta0)**2
!
!V(Urey-Bradley) = Kub(S - S0)**2
!
!Ktheta: kcal/mole/rad**2
!Theta0: degrees
!Kub: kcal/mole/A**2 (Urey-Bradley)
!S0: A
!
HH2S SH2S HH2S 65.136 92.50 ! 0.00 0.00000
AUC AUC AUC 0.000 0.000
DIHEDRALS
!
!V(dihedral) = Kchi(1 + cos(n(chi) - delta))
!
!Kchi: kcal/mole
!n: multiplicity
!delta: degrees
!
!atom types Kchi n delta
!
!Heme to Sulfate (PSUL) link
AUC AUC AUC AUC 0.00 1 0.000 !
IMPROPER
!
!V(improper) = Kpsi(psi - psi0)**2
!
!Kpsi: kcal/mole/rad**2
!psi0: degrees
!note that the second column of numbers (0) is ignored
!
!atom types Kpsi psi0
AUC AUC AUC AUC 0.000 0 0.000
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
!adm jr., 5/08/91, suggested cutoff scheme
!
!V(Lennard-Jones) = Eps,i,j[(Rmin,i,j/ri,j)**12 - 2(Rmin,i,j/ri,j)**6]
!
!epsilon: kcal/mole, Eps,i,j = sqrt(eps,i * eps,j)
!Rmin/2: A, Rmin,i,j = Rmin/2,i + Rmin/2,j
!
!atom ignored epsilon Rmin/2 ignored eps,1-4 Rmin/2,1-4
!
!carbons
HH2S 0.000000 0.000000 0.000000 ! H2S Hydrogen
!
SH2S 0.000000 -0.461000 2.087500 ! H2S Sulfur
!
AUC 0.000000 0.039000 1.036800 0.000000 0.039000 1.036800
!
Your kind help is highly appreciated in advance.
*
-- Yours Sincerely, Kiarash Hosseini Mechanical Engineering MSc Tehran Iran
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