On 12/02/2011 12:22 PM, Justin A. Lemkul wrote:
Do the -ci and -cs steps separately and see if that gives you the
proper output. I have found that the two are incompatible, but in
theory, I don't know why one couldn't do everything in one step.
It can depend on the assumptions about the purpose of -cs and -ci. If
-ci is being used to insert some ions or small molecules then you want
to do -cs first lest you create larger interstices via the VDW
exclusions. If -ci inserts large molecules, then you want to do that
first. The observations of the OP suggest the former is implemented.
Mark
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