Yun Shi wrote:
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
interactions.
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 off?
You should use the cutoff described the authors of the force field, in this case
rvdw=1.4. Unless you can demonstrate that by using a different value you can
achieve superior results, stick with the specifics of parameterization. I have
never seen ill effects of setting rvdw=1.4 and using dispersion correction with
this force field.
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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