VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Wed Aug 31 2011 - 07:45:45 CDT

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On Wed, Aug 31, 2011 at 4:12 AM, hamid mosaddeghi
<hamid592004m_at_yahoo.com> wrote:
> 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?

there are a _ton_ of possible reasons.

> I used Cutoff angle 30 and cutoff distance 3.5 A from literatures.

that still doesn't mean you are using the exact same definition of
hydrogen bonds, and more importantly, it doesn't say anything about
whether your simulation has been properly equilibrated and is simulating
the exact same region in phase space. did you do any statistical error
estimates?

axel.

> Best regards
>
> Hamid Mosaddeghi
>
> Phd Student Of Physical Chemistry

-- 
Dr. Axel Kohlmeyer
akohlmey_at_gmail.com  http://goo.gl/1wk0
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.

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