<div dir="ltr">Dear gromacs users,<br><br>I am trying to pull a ligand out of a cavity of a membrane protein (along the Z axis).<br>Problem is, that with every pull settings I have tried the ligand gets "stuck" on the protein's center of mass. How can I make it go all the was to the bulk water?<br>
It always gets stuck on the COM. And I've tried using both umbrella and constant force, so I'm getting the feeling that I'm missing something trivial.<br><br>Here's an example of one set of pull-parameters I tried:<br>
-------------------------------><br><span style="font-family: courier new,monospace;">pull = constant_force</span><br style="font-family: courier new,monospace;"><span style="font-family: courier new,monospace;">pull_geometry = distance</span><br style="font-family: courier new,monospace;">
<span style="font-family: courier new,monospace;">pull_dim = N N Y</span><br style="font-family: courier new,monospace;"><span style="font-family: courier new,monospace;">pull_start = yes ; define initial COM distance > 0</span><br style="font-family: courier new,monospace;">
<br style="font-family: courier new,monospace;"><span style="font-family: courier new,monospace;">pull_ngroups = 1</span><br style="font-family: courier new,monospace;"><span style="font-family: courier new,monospace;">pull_group0 = Protein </span><br style="font-family: courier new,monospace;">
<span style="font-family: courier new,monospace;">pull_group1 = Ligand </span><br style="font-family: courier new,monospace;"><span style="font-family: courier new,monospace;">;pull_rate1 = -0.001 ; 0.01 nm per ps = 10 nm per ns</span><br style="font-family: courier new,monospace;">
<span style="font-family: courier new,monospace;">pull_k1 = 1000 ; kJ mol^-1 nm^-2</span><br><------------------------------<br><br>Can anyone help enlighten me as to what I am doing wrong?<br>Thanks,<br>
-Shay<br><br>P.S.<br>Using gromacs 4.0.7.<br></div>