[gmx-users] Calculating bond energy

[Yulia Einav]

Thank you for your reply, Mark.
My protein has four disulfide bonds. I did in silico mutation of one of them and, then, MD simulations. Now I want to know whether breaking one bond influence the others. I can measure the distance between the centers of mass of two sulfur atoms, but is it sufficient to supply the information about bond strength of each disulfide? I guess I mean the bond dissociation energy (not the average one, but rather for each bond individually) of the remaining S-S bonds in the protein.
Thanks!
 
Yulia Einav Ph.D. 
 
Mathematical Biology Unit
Department of Applied Mathematics
Faculty of Sciences, H.I.T. 
52 Golomb Str. POB 305, Holon 58102, Israel.
Tel. 972-3-5026769, Fax. 972-3-5026769
E-mail: yulia_e at hit.ac.il, Web: http://www.hit.ac.il <http://www.hit.ac.il/> 

________________________________

From: gmx-users-bounces at gromacs.org on behalf of Mark Abraham
Sent: Wed 5/28/2008 14:53
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Calculating bond energy



Yulia Einav wrote:
> Dear Gromacs users,
>
> After performing MD simulations I want to calculate bond energy for the
> disulfide bond present in the simulated structure. I didn't find the
> option for doing this under g_energy command. Does any one know how to
> do this type of analysis?

"Calculate bond energy" is too vague... it might been any number of
things. Can you clarify what you're trying to do, please?

Mark
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