[gmx-users] setting vdw cutoff with specific force-filed?

Yun Shi yunshi09 at gmail.com
Thu Aug 4 06:53:46 CEST 2011

Hi all,

I am working with GROMOS 53a6 ff in GROMACS 4.5, and I assume a
Lennard-Jones interaction function was used for short-range vdw

>From the reference paper *A Biomolecular Force Field Based on the Free
Enthalpy of Hydration and Solvation: The GROMOS Force-Field Parameter Sets
53A5 and 53A6*, I found that for example,

when rvdw = 1.5nm, the repulsion term of the interaction between two CH1
type atoms (C12ij = 9.85^2) can be calculated as 9.850*9.850 / (1.5^12) =
0.747786 kJ/mol. So I wonder if this value is considered to be small enough
to be ignored.

In addition, it seems not until 5 nm does the dispersion term become larger
than the repulsion term in this case, so would turning on Dispersion
Correction between, say 1.5 to 5 nm introduce more errors than turning it

Any suggestion would be appreciated!


Yun Shi
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