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-012.96E-01
LO LOM 1 1.10E-012.96E-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-011.10E-01
LO LOM 1 2.96E-011.10E-01
LO opls_1161 3.06E-019.47E-02
LO LNL 1 3.10E-019.88E-02
LO LC 1 3.33E-017.76E-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
--
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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