CHARMM Development Project
Posted By: mou Deletion of overlap between water boxes - 03/31/07 09:20 AM

I want to delete the overlap between two water boxes.
I have uesd the command "delete atom seli ( .byres. ( segi sol .and. type o1 .and. ( ( .not. segi sol .and. hydrogen ) .around. 2.6 ) ) ) end"
where sol is the new water box which is translated anong bilayer normal & make an overlap of 6A with the previous water box.But after deletion a gap is generated at the interface of two boxes,smaller but a significant gap persist even if the deletion distance is reduced to 2.4. Can I further reduce the distance to 2.2 or 2 or use another command? Any suggestion will be highly appreciated.
With thanks
Moutusi Manna
Posted By: rmv Re: Deletion of overlap between water boxes - 03/31/07 04:25 PM
You can reduce the cutoff used for .around. as needed for your situation. It's easy to tell if it's too small; you'll have too many bad VDW overlaps. I've used 1.8 at times for water deletions.
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