Creating a parameter file for SiC nanotube

From: zeynab hosseini (
Date: Fri Aug 26 2022 - 11:46:36 CDT

Dear All,

I want to equilibrate a system composed of Silicon Carbide nanotube (SiCNT)
solvated in a simple water box. I need to create a CHARMM-adapted parameter
file. I took the parameter
<;!!DZ3fjg!4iRK54Wv9r3jOX7o2kHpVa4fsgbbKv2L8fT1skOF843UED6EXCmbo08T5n8l9FiynHuZUTuAI5INRsDPqcPU9oF3Xvs7$ >s
from this reference <;!!DZ3fjg!4iRK54Wv9r3jOX7o2kHpVa4fsgbbKv2L8fT1skOF843UED6EXCmbo08T5n8l9FiynHuZUTuAI5INRsDPqcPU9rwoTDfx$ > which is used
by several other works, like this
<;!!DZ3fjg!4iRK54Wv9r3jOX7o2kHpVa4fsgbbKv2L8fT1skOF843UED6EXCmbo08T5n8l9FiynHuZUTuAI5INRsDPqcPU9hzO5YHd$ >, successfully. The
<;!!DZ3fjg!4iRK54Wv9r3jOX7o2kHpVa4fsgbbKv2L8fT1skOF843UED6EXCmbo08T5n8l9FiynHuZUTuAI5INRsDPqcPU9gPWEj4q$ >
I created is as follows. CI stands for carbon type and SI for silicon type
in Si-C bond.

MASS -1 CI 12.01100
MASS -1 SI 28.0855

!V(bond) = Kb(b - b0)**2
!Kb: kcal/mole/A**2
!b0: A
!atom type Kb b0
!silicon section
SI CI 299.04 1.783

!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
!atom types Ktheta Theta0 Kub S0
CI SI CI 47.54 119.00 !

!V(dihedral) = Kchi(1 + cos(n(chi) - delta))
!Kchi: kcal/mole
!n: multiplicity
!delta: degrees
!atom types Kchi n delta
!For SiC
CI SI CI SI 0.35 3 180.0 !
!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

SI 0.0 -0.5850 1.904 0.000000 -0.5850 1.904

CI 0.0 -0.0559 1.910 0.000000 -0.0559 1.910

I performed the simulation and it worked but as soon as I minimized the
system energy, the SiCNT deforms. I wonder what I missed as the works by
other people went well but mine (image
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I also attached the configuration and othe needed files in the following:;!!DZ3fjg!4iRK54Wv9r3jOX7o2kHpVa4fsgbbKv2L8fT1skOF843UED6EXCmbo08T5n8l9FiynHuZUTuAI5INRsDPqcPU9lLt8pRt$;!!DZ3fjg!4iRK54Wv9r3jOX7o2kHpVa4fsgbbKv2L8fT1skOF843UED6EXCmbo08T5n8l9FiynHuZUTuAI5INRsDPqcPU9l2Is9sw$;!!DZ3fjg!4iRK54Wv9r3jOX7o2kHpVa4fsgbbKv2L8fT1skOF843UED6EXCmbo08T5n8l9FiynHuZUTuAI5INRsDPqcPU9k2Yb_hj$;!!DZ3fjg!4iRK54Wv9r3jOX7o2kHpVa4fsgbbKv2L8fT1skOF843UED6EXCmbo08T5n8l9FiynHuZUTuAI5INRsDPqcPU9i_5fcQg$

Any assistance would be really appreciated,

All the best,


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