VMD-L Mailing List
From: hamid mosaddeghi (hamid592004m_at_yahoo.com)
Date: Fri Sep 02 2011 - 05:46:16 CDT
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Dear Jacob
if I used angle from 44 to 46 , I get 3.2 hbond per water molecule. I work on confined fuild and test it for confined system but this method is wrong because based on paper I expect reduce number hbond in confined water but if I used angle 44 to 46 number of hbond increase from 3.2 in bulk to 3.4 , this result is wrong, but if I used angle 30 ,I see trend base on papers, but result about number of hbond less than of them.
Best Regards
From: "Goldsmith, Jacob" <jgoldsmith_at_uky.edu>
To: hamid mosaddeghi <hamid592004m_at_yahoo.com>
Sent: Friday, September 2, 2011 4:02 AM
Subject: RE: vmd-l: Hbond in VMD
i did this a long time ago... i'll look up my notes and send what i can. i think the angle is more like 44 to 46. The angle is not calculated the way the literature does the calculation. Again, look at the source and i'll try to repost soon
-j
________________________________________
From: owner-vmd-l_at_ks.uiuc.edu [owner-vmd-l_at_ks.uiuc.edu] On Behalf Of hamid mosaddeghi [hamid592004m_at_yahoo.com]
Sent: Wednesday, August 31, 2011 1:29 PM
To: vmd
Subject: Fw: vmd-l: Hbond in VMD
Dear Goldsmith
Please explain "Hbonds in VMD use a very non standard angle"? what should I do to solve this problem? or how can I define these Cutoff angle 30 and cutoff distance 3.5 A exactly for software?
Best Regards.
From: ", Jacob" <jgoldsmith_at_uky.edu>
To: hamid mosaddeghi <hamid592004m_at_yahoo.com>
Sent: Wednesday, August 31, 2011 5:55 PM
Subject: RE: vmd-l: Hbond in VMD
Hbonds in VMD use a very non standard angle, not necessarily the angle your thinking of. Look at the source code for more information.
-J
________________________________________
From: owner-vmd-l_at_ks.uiuc.edu<mailto:owner-vmd-l_at_ks.uiuc.edu> [owner-vmd-l_at_ks.uiuc.edu<mailto:owner-vmd-l_at_ks.uiuc.edu>] On Behalf Of hamid mosaddeghi [hamid592004m_at_yahoo.com<mailto:hamid592004m_at_yahoo.com>]
Sent: Wednesday, August 31, 2011 4:12 AM
To: vmd
Subject: vmd-l: Hbond in VMD
Dear all
I counted Hbond from VMD for SPC/E water model in normal condition , I got 2.56 Hbond per/molcule but more paper reported 3.~ 3.3 Hbond per/molcule why?
I used Cutoff angle 30 and cutoff distance 3.5 A from literatures.
Best regards
Hamid Mosaddeghi
Phd Student Of Physical Chemistry
- Next message: siladitya mukherjee: "Re: Movie maker in VMD"
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- Maybe in reply to: Axel Kohlmeyer: "Re: Hbond in VMD"
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