[gmx-users] g_energy -fee -inf problem

[Naser, Md Abu]

Hi Mark,

Thank you very much for your replay.I was just trying to 
calculate free energy difference between reduced protein and non-reduced 
protein solvated in water(spc) using ffG43a2 force field. 

Abu Naser 

School Of Life Sciences 
Heriot-Watt University 
Edinburgh EH14 4AS 
Email: mn2 at hw.ac.uk
Phone: +44(0)1314518265 
Fax : +44(0) 131 451 3009 


 



-----Original Message-----
From: gmx-users-bounces at gromacs.org on behalf of Mark Abraham
Sent: Sat 22/09/2007 6:05 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] g_energy -fee -inf problem
 
Naser, Md Abu wrote:
> Hi All User,
> 
> I am getting free energy difference -inf.
> 1st I run a protein in water molecule and then I made a different
> topology file with deleting 4 disulfide bonds and accordingly the angles and
> diherdal angles.

What physical model are you trying to reproduce here?

> Then, I run -rerun for the both and and g_energy -fee, 
> which
> giving me free energy difference -inf.
> 
> Can anyone please point me out where I am making mistakes.

Mark
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