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<TITLE>RE: [gmx-users] g_energy -fee -inf problem</TITLE>
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<P><FONT SIZE=2>Hi Mark,<BR>
<BR>
Thank you very much for your replay.I was just trying to<BR>
calculate free energy difference between reduced protein and non-reduced<BR>
protein solvated in water(spc) using ffG43a2 force field.<BR>
<BR>
Abu Naser<BR>
<BR>
School Of Life Sciences<BR>
Heriot-Watt University<BR>
Edinburgh EH14 4AS<BR>
Email: mn2@hw.ac.uk<BR>
Phone: +44(0)1314518265<BR>
Fax : +44(0) 131 451 3009<BR>
<BR>
<BR>
<BR>
<BR>
<BR>
<BR>
-----Original Message-----<BR>
From: gmx-users-bounces@gromacs.org on behalf of Mark Abraham<BR>
Sent: Sat 22/09/2007 6:05 PM<BR>
To: Discussion list for GROMACS users<BR>
Subject: Re: [gmx-users] g_energy -fee -inf problem<BR>
<BR>
Naser, Md Abu wrote:<BR>
> Hi All User,<BR>
><BR>
> I am getting free energy difference -inf.<BR>
> 1st I run a protein in water molecule and then I made a different<BR>
> topology file with deleting 4 disulfide bonds and accordingly the angles and<BR>
> diherdal angles.<BR>
<BR>
What physical model are you trying to reproduce here?<BR>
<BR>
> Then, I run -rerun for the both and and g_energy -fee,<BR>
> which<BR>
> giving me free energy difference -inf.<BR>
><BR>
> Can anyone please point me out where I am making mistakes.<BR>
<BR>
Mark<BR>
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