Previous Thread
Next Thread
Print Thread
Deletion of overlap between water boxes
#13938 03/31/07 09:20 AM
Joined: Mar 2007
Posts: 7
M
mou Offline OP
Forum Member
OP Offline
Forum Member
M
Joined: Mar 2007
Posts: 7

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

Re: Deletion of overlap between water boxes
mou #13939 03/31/07 04:25 PM
Joined: Sep 2003
Posts: 8,547
Likes: 3
rmv Offline
Forum Member
Offline
Forum Member
Joined: Sep 2003
Posts: 8,547
Likes: 3
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.


Moderated by  lennart, rmv 

Link Copied to Clipboard
Powered by UBB.threads™ PHP Forum Software 7.7.4
(Release build 20200307)
Responsive Width:

PHP: 5.6.33-0+deb8u1 Page Time: 0.007s Queries: 18 (0.003s) Memory: 0.8940 MB (Peak: 0.9590 MB) Data Comp: Off Server Time: 2021-05-18 10:23:10 UTC
Valid HTML 5 and Valid CSS