<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>Hi,</div><div> I am trying to calculate the PMF of two peptides using constraint in gromacs 4.0.5. But, I am finding a very large oscillation( from -1000 to +1000) in the force that is being printed in pullf.xvg file . Is this oscillation normal ? In that case at any distance, the mean force will be zero ( I assume).</div><div><br></div><div>Here is the excerpt of the mdp file:</div><div><div>; pull code</div><div>pull = constraint</div><div>pull_geometry = distance</div><div>pull_dim = Y Y Y</div><div>pull_init1 = 1.5</div><div>pull_k1
=</div><div>pull_group0 = CA1</div><div>pull_ngroups = 1</div><div>pull_group1 = CA2</div><div>pull_nstxout = 50 ;step</div><div>pull_nstfout = 20</div><div><br></div><div>Thanks</div><div>Jagannath</div></div><div style="position:fixed"></div>
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