Dear All,<div><br></div><div>I have tried to calculate the free energy of binding using Jarzynski equality. I employed the following procedure.</div><div><br></div><div>--I did force pulling simulations along Z-direction as exemplified in Justin's umbrella sampling simulations. I did 50, 250 and 500 pulling simulations to test the convergence and also two different pulling rates (2nm/ns and 4nm/ns), two different force </div>
<div> constants (2000 kJ mol^-1 nm^-2 and 4000 kJ mol^-1 nm^-2).</div><div><br></div><div>--From the pulling simulation, I get the pullf.xvg and pullx.xvg. </div><div><br></div><div>--I use the force from pullf.xvg and calculate the work at each time step by multiplying with v*dt and calculate average work for each simulation.</div>
<div><br></div><div>--Once I have the work for each simulation, I calculate the exp(-beta*W) for each simulation and calculate the average of exp(-beta*W). </div><div><br></div><div>--Once I have the average of exp(-beta*W), I calculate the free energy delF = -kB*T ln(exp(-beta*W)).</div>
<div><br></div><div>The question I have is whether my approach for calculating the work is correct/feasible or not.</div><div>Does the pullf.xvg written by mdrun during a pulling simulation contain the pull force only?</div>
<div>Do I need to add any corrections?</div><div>I'm doing NPT simulations, so can I add the pdV correction as suggested in one of the paper (<span class="Apple-style-span" style="font-family: 'Trebuchet MS', Arial, Helvetica, sans-serif; font-size: 12px; line-height: 16px; "><cite><span class="Apple-style-span" style="font-style: normal; ">Macromolecules</span></cite>, <span class="citation_year">2008</span>, <span class="citation_volume">41</span> (6), pp 2283–2289</span>) by Berk Hess? Or did I understand the paper incorrectly?</div>
<meta http-equiv="content-type" content="text/html; charset=utf-8"><div><br></div><div>For a publication level of work, I'll use NVT ensemble. But for now my biggest concern is calculation of work.</div><div><br></div>
<div>Any suggestions will be greatly helpful.</div><div><br></div><div>Thanks for you time,</div><div><br></div><div>Sai Ramadugu</div><div>Dept of Chemistry,</div><div>University of Iowa.</div><div><br></div><div><br></div>
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