VMD-L Mailing List

From: Martin, Erik W (Erik.Martin_at_stjude.org)
Date: Wed Nov 21 2012 - 08:58:11 CST

Calculating the "strength" of a h-bond is a non-trivial task and certainly beyond the scope of VMD. A lot of people do sort of a hand waving estimation where they will assume that shorter distance, linear h-bonds are relatively stronger. However, this does not always bare out to be the case. The only real way to get to the root of this issue is to preform QM calculations with a program like Gaussian and look at the coupling between H-bonding nuclei.

-Erik
________________________________________
From: owner-vmd-l_at_ks.uiuc.edu [owner-vmd-l_at_ks.uiuc.edu] On Behalf Of Ajasja Ljubetič [ajasja.ljubetic_at_gmail.com]
Sent: Tuesday, November 20, 2012 7:05 AM
To: 肖富贵
Cc: vmd
Subject: Re: vmd-l: How to calculate the Hydrogen bond strengh. .

Are you sure you have sent this message to the right mailing list? I have my doubts...

VMD itself can not calculate H-bond strengths (as far as I know).

Regards,
Ajasja

On 20 November 2012 13:10, 肖富贵 <helitrope_at_163.com<mailto:helitrope_at_163.com>> wrote:
Hi guys,
Is there a method to calculate the strengh of a hydrogen bond. There is a carbonyl grouop with two hydrogen bonds, and i guess these two hydrogen bonds have different strengh, so is there an accurate way to calculate it?
Best wishes
Fugui

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