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

From: JťrŰme Hťnin (jhenin_at_ifr88.cnrs-mrs.fr)
Date: Wed Jan 20 2010 - 07:05:37 CST

Well, you have to factor this into Rmin. If you set Rmin^6 =
2*(sigma^6), you'll see it starts to work out nicely. You have to
write down the calculation cleanly, of course.

Best,
Jerome

2010/1/20 Áéčś£Ĺ <corarbor_at_163.com>:
> Hi, J√©r√īme:
> Thank you for sharing.
> How do you deal with the coefficient 2 in front of ^6 in NAMD's VDW
> expression
> "V(Lennard-Jones) = Eps,i,j[(Rmin,i,j/ri,j)**12 - 2(Rmin,i,j/ri,j)**6]"
> while this coefficient 2 is absent in gromacs' style.
>
> best
> Shen Wang
>
> Śú®2010-01-20¬†17:27:42ÔľĆ"J√©r√īme¬†H√©nin"¬†<jhenin_at_ifr88.cnrs-mrs.fr>¬†ŚÜôťĀďÔľö
>>Hi,
>>CHARMM and NAMD use kcal/mol (i.e. 4184 J/mol) for energies and
>>Angstrom for distances.
>>Best,
>>Jerome
>>
>>2010/1/20¬†Áéčś£Ĺ¬†<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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