From: Íõ—² (corarbor_at_163.com)
Date: Wed Jan 20 2010 - 00:24:27 CST
I am trying to run a carbon nanotube related MD which was originally run with Gromacs. I would like to set the carbon parameter exactly the same as that in Gromacs. I've learned that the VDW parameter I used in gromacs is as below:
[ atomtypes ]
;type mass charge ptype sigma epsilon
CN 12.01100 0.000 A 0.2232E-02 0.34480E-05
,which means the pair VDW potential can be written as :
while sigma is 0.2232E-02 Kj/mol and sigma is 0.34480E-05nm.
However in NAMD different expression for VDW is applied:
!V(Lennard-Jones) = Eps,i,j[(Rmin,i,j/ri,j)**12 - 2(Rmin,i,j/ri,j)**6]
!atom ignored epsilon Rmin/2
CA 0.000000 -0.070000 1.992400
I have no idea about the unit of epsilon and Rmin/2 in this expression. I tried searching the NAMD user's guide and failed to find the answer. Please figure out this for me or tell me which reference I should turn to.
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