[gmx-users] genbox error

Mark Abraham Mark.Abraham at anu.edu.au
Sat Feb 12 02:39:34 CET 2011

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.


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