[gmx-users] cutoff problem

Justin A. Lemkul jalemkul at vt.edu
Wed Mar 24 20:26:15 CET 2010

Qian Wang wrote:
> Hi,
> I want to test different values of cutoff for vdw. However, in the list 
> someone said cutoff = 0.9 for vdw was used for paramaterizing of Gromos 
> force field, other values would cause error, and also there was someone 
> saying that cutoff for vdw should be set to 1.4. Can someone make this 
> question clear? Thanks a lot.

It is always helpful to post the URL's to the posts where you found this 
information.  If your goal is to test different cutoff values, you should be 
able to sort out sources of error.  Have a look at the original literature.  For 
example, in the citation for the 53A5/53A6 parameter sets:

"...the parameters used to describe the van der Waals interactions in the 
liquids perform well in combination with the (recently developed) aliphatic van 
der Waals parameters.  All have now been parameterized with a cutoff of 1.4 nm."

Furthermore, that paper describes the appropriate cutoffs for neighborsearching 
and short-range Coulombic interactions, although the latter is somewhat flexible 
in conjunction with PME, which was not used in the original derivation.


> Qian


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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