<html><head><style type="text/css"><!-- DIV {margin:0px;} --></style></head><body><div style="font-family:'times new roman', 'new york', times, serif;font-size:12pt"><div><span class="Apple-style-span" style="font-family: times, serif; "><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Hi,</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "> I would like to use constraint force pull code to calculate the free energy of association of two peptide using the distance between <span class="yshortcuts" id="lw_1271868255_0">center of mass</span> of two peptides as reaction coordinate. I am planning to use gromacs 4. </div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Here I have some queries:</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">1. Since I will constraint
method, I guess, I do not have to use any force-constant ( unlike umbrella sampling) . If that is correct, do I need to specify a pulling rate ? If so, what will be a typically appropriate range of value to start with ?</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">2. In umbrella sampling technique, we check the overlap of position histogram of two consecutive windows to check the convergence . Here , using constraint force technique, what should I check for convergence. Is that the force ?</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">3. Once I get <span class="yshortcuts" id="lw_1271868255_1">time series</span> of force for all windows, how
should I unbias the effect of constraint and what formula I should use to integrate the force? Is that integration implemented in gromacs ?</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Thanks</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Sanku</div></span></div><div style="position:fixed"></div>
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