From: Jérôme Hénin (jhenin_at_ifr88.cnrs-mrs.fr)
Date: Wed Jan 20 2010 - 03:27:42 CST
CHARMM and NAMD use kcal/mol (i.e. 4184 J/mol) for energies and
Angstrom for distances.
2010/1/20 çŽ‹æ£½ <corarbor_at_163.com>:
> Hello everyone:
> I am trying to run a carbon nanotube related MD which was originally run
> with Gromacs. I would like to setÂ the carbon parameter exactly the same as
> that in Gromacs. I've learned that the VDW parameter I used in gromacs is as
> [ atomtypes ]
> ;typeÂ Â Â massÂ Â Â chargeÂ Â ptypeÂ Â sigmaÂ Â Â Â Â epsilon
> Â CNÂ Â Â 12.01100Â Â 0.000Â Â Â Â Â Â AÂ 0.2232E-02Â Â 0.34480E-05
> ,which means the pair VDW potential can be written as :
> while sigma is 0.2232E-02 Kj/mol and sigma isÂ 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]
> !atomÂ ignoredÂ Â Â epsilonÂ Â Â Â Â Rmin/2
> CAÂ Â Â Â 0.! 000000Â -0.070000Â Â Â Â 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.Â Please
> figure out this for me or tell me which reference I should turn to.
> Many thanks.
> Shen Wang
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