[gmx-users] vdW cutoff

[Justin A. Lemkul]

Fabian Casteblanco wrote:
> Hello,
> 
> I am quite confused on whether it is better to use a standard cut-off
> scheme for vdW interactions or if its better to use a switch or shift
> function for this.  I am doing a free energy calculation on the
> solvation of a drug molecule in a solvent (on CHARMM ff) so I want to
> be as accurate as possible.  The CHARMM paper does state that they use
> some type of switch function between 10 A and 12 A but I'm confused on
> the difference between 'Switch' and 'Shift'.  I ran the solvents alone

They're fundamentally the same.  See the discussion in the manual, section 4.1.5.

> using these different types and it seems to give similar results.  Is
> this a major decision to getting accurate free energy calculations?
> Will using standard 14 A cutoffs with DispersionCorrection=EnerPres be
> enough?
> 

You should stick with the prescribed force field methodology unless you can 
demonstrate your modified method is (a) equivalent or (b) superior.  In any 
case, you need a well-defined test case (i.e. something trusted and probably 
published and therefore thoroughly vetted) that you can play with until you're 
satisfied that your method is sufficiently accurate.  Reviewers want 
justification for deviations from what is expected.  At least, they should :)

-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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