[gmx-users] Fwd: Problem with generating topology file for OPLS force field for membrane protein simulation

[Justin Lemkul]

On 4/15/13 6:25 AM, Parul tew wrote:
> Dear GMX users,
>   I am working on a protein which I want to simulate in a lipid bilayer
> environment (POPC) and want to use OPLS force field for the same. I wanted
> to modify the parameter files of lipids taken from peter teilman site.
> Taking cue from chris neale (may 2006 gmx mailing list) I changed the c6
> and c12 to sigma epsilon using formula
> Sigma = (c12/c6)^1/6
> and
> epsilon = c6/(4*sigma^6)
> i tried it for the [pairtypes] in lipid.itp file, but the calculations I
> made using excel gave me the following:
>
> [ pairtypes ]
> ;       i       j       funct   sigma           epsilon
>          LO      LO      1       1.10E-01        2.96E-01
>          LO      LOM     1       1.10E-01        2.96E-0
>
>
> and so on i.e. the values of sigma and epsilon are interchanged, as
> opposed to the values listed by chris neale in archive mail (listed
> below)
>
> [ pairtypes ]
>
> ;       i       j       funct   sigma           epsilon
>          LO      LO      1       2.96E-01        1.10E-01
>          LO      LOM     1       2.96E-01        1.10E-01
>          LO      opls_116        1       3.06E-01        9.47E-02
>          LO      LNL     1       3.10E-01        9.88E-02
>          LO      LC      1       3.33E-01        7.76E-02
> etc...
>
> I am doing something wrong or I can just interchange the values and
> use them accordingly.
>

I think you're doing the calculation wrong, but I can't say exactly how.  If I 
calculate (1.987E-7 / 2.952E-4) ^ (1/6), it comes out to the correct sigma value 
of 0.29603763.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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