Re: How to convert the GROMOS parameter unit into charmm22 style

From: Jrme Hnin (jhenin_at_ifr88.cnrs-mrs.fr)
Date: Wed Jan 20 2010 - 03:27:42 CST

Hi,
CHARMM and NAMD use kcal/mol (i.e. 4184 J/mol) for energies and
Angstrom for distances.
Best,
Jerome

2010/1/20 王棽 <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 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 :
> V(ij)=4*sepsilon*[(r/sigma)^12-(r/sigma)^6]
> 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.
> Many thanks.
>
> Shen Wang
>
>
>

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