<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: arial; font-size: 13px; ">Hi,<br><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">I am studying Potential of mean force(PMF) of association of two peptides. I want to decompose the PMF into energy(enthalpy) and entropic terms. But, I have some queries on how to extract those contributions .</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "> </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; "> I found, in literature, generally, people try to get the energy(enthalpy) first and then subtract it
from PMF to get the entropic contribution. My question is related to how to get the energy term first:</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; ">1. Will it be appropriate to just use g_energy tool on ener.edr file for each windows obtained from umbrella sampling and select the '<span class="yshortcuts" id="lw_1286983971_0" style="color: rgb(54, 99, 136); border-bottom-style: dotted; border-bottom-width: 2px; border-bottom-color: rgb(54, 99, 136); cursor: pointer; ">potential energy</span>' functionality term to get the *average potential energy* for each windows ? </div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">I used energy groups = system in the .mdp file for each windows of my umbrella sampling simulations.</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. If it is so, now I wonder whether g_energy will give that potental energy *in presence of umbrella bias* . If it is true, do one need to first unbias the energy some how ( like using a boltzman factor) ? However, I do not how to do that. </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; ">if you provide any ideas, that will be great . </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; "><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Here is the
details on what I have done to get the PMF .</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "> </div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "> I am studying Potential of mean force(PMF) of association of two peptides. For this purpose , I have carried out GROMACS 4.0.7 umbrella sampling simulation by dividing the reaction coordinate( i.e distance between center of mass of two peptides) into around 25 windows of 0.1 nm separation. Now, I have used WHAM and got the PMF by unbiasing the umbrella potential.</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; ">Sanku</div></div></span></div><div style="position:fixed"></div>
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