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

[Justin A. Lemkul]

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

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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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