VMD-L Mailing List
From: sajad falsafi (sajad.falsafi_at_yahoo.com)
Date: Fri Oct 14 2011 - 08:06:08 CDT
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- In reply to: subrata paul: "hbond analysis"
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Hi,
you should type this command in TkConsole for calculating H-bonds of water: hbonds -sel1 [atomselect top "water"]
* if sel1 and sel2 overlap, hbonds output is unreliable!
also you can read all information about using the HBonds Plugin in this address: http://www.ks.uiuc.edu/Research/vmd/plugins/hbonds/ .
Sajad Falsafi & Zahra Karimi
>________________________________
>From: subrata paul <paul.subrata34_at_gmail.com>
>To: vmd-l_at_ks.uiuc.edu
>Sent: Friday, October 14, 2011 12:41 PM
>Subject: vmd-l: hbond analysis
>
>
>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 youSubrata Paul
>IITGuwahati
>India Assam
>
>
>
>
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