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.
Thanking you
Parul Tewatia
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