<div>Dear Mark,</div>
<div> </div>
<div>I used thermodynamics integration method (TI) to obtain delta Gibbs energy of the protein membrane with dual topology. <font face="NimbusRomNo9L-Regu" size="3"><font face="NimbusRomNo9L-Regu" size="2"></font></font></div>
<p>topology A (lambda=0) to topology B (lambda=1)</p>
<div>What i obtained after using mdrun command to calculate free energy is dgdl.xvg that contain dV(total)/dlamda via time. I want to obtein dV(bond)/dlamda and dV(non-bond)/dlamda, seperetly. dV(bond)/dlambda and dV(non-bond)/dlambda are not writed in free.edr and free.log. how to produce dv(bond)/dlambda and dV(non-bond)/dlambda.</div>
<div>my version gromacs is 4.0.5 and 4.0.7.</div>
<div> </div>
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<div>Thanks in advance,</div>
<div>Maleki<br><br></div>
<div class="gmail_quote">On Tue, Aug 9, 2011 at 6:18 AM, Mark Abraham <span dir="ltr"><<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>></span> wrote:<br>
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<div class="im">On 9/08/2011 9:13 PM, afsaneh maleki wrote:
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<p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt; LINE-HEIGHT: 200%"><font face="Times New Roman" size="3">Hi,</font></p>
<p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt; LINE-HEIGHT: 200%"><font face="Times New Roman" size="3"> </font></p>
<p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt; LINE-HEIGHT: 200%"><font face="Times New Roman" size="3">I used thermodynamics integration method (TI) to obtain delta Gibbs energy of the protein membrane. I want to separate contributions of delta bonding and nonbonding energy in delta Gibbs energy.</font></p>
</blockquote><br></div>So instead of using the sum of bonded and non-bonded energy (i.e. total PE), use them separately. Whether that will mean anything is up to you to demonstrate.<br><br>Mark<br><br>
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<p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt; LINE-HEIGHT: 200%"><font face="Times New Roman" size="3"> </font></p>
<p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt; LINE-HEIGHT: 200%"><font face="Times New Roman" size="3">Best wishes,</font></p>
<p class="MsoNormal" style="MARGIN: 0cm 0cm 0pt; LINE-HEIGHT: 200%"><font face="Times New Roman" size="3">Maleki,</font></p><br>
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