VMD-L Mailing List

From: subrata paul (paul.subrata34_at_gmail.com)
Date: Fri Oct 14 2011 - 04:11:46 CDT

Dear Sir
I am a student of phd and new in VMD.When I went through the VMD mailing
list.
I am using amber10. I loaded my trejectory and try to calculate but I could
not.I think my command line is wrong.

I want to calculate water-water hbond.
measure hbonds 3.5 30 -sel1 [atomselect top "water"] -sel2 [atomselect top
"water']
Is this correct?
How to finde hbond/molecule
Can you help me, giving me a example of hbond command line?

Can you suggest me How can we do hbond vs time?

Any help would be greatly appreciated!
very very Thanking you
Subrata Paul
IITGuwahati
India Assam