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.
-Justin
Qian
--
========================================
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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