<div dir="ltr">Dear Gromacs Users,<br><br>I've done Justin's tutorial regarding PMF/umbrella sampling and now, when approaching my own system I have a couple of questions.<br>(Link to the tutorial here: <a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/06_umbrella.html" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/06_umbrella.html</a> )<br>
<br>My system is comprise of a transport protein (embedded in membrane) and a ligand. The system is positions so that Z axis is the axis on which I've made PMF windows.<br>The next step on this is to run these windows separately and I didn't quite understand why in step-6 of the tutorial it specifies to still use <span style="font-family: courier new,monospace;">pull_dim = N N Y</span> and <span style="font-family: courier new,monospace;">pull_rate1 = 0.0.</span><br>
<br>As far as I understood, during the production run we want to sample the Z position. Shouldn't then it use <span style="font-family: courier new,monospace;">pull_dim = Y Y N</span> ?<br>And what does it mean to the system when we set <span style="font-family: courier new,monospace;">pull_rate1 = 0.0</span> ?<br>
Does it mean that when <span style="font-family: courier new,monospace;">pull_dim = N N Y</span> and<span style="font-family: courier new,monospace;"> pull_rate1 = 0.0</span> it restrains <span style="font-family: courier new,monospace;">pull_group0</span> on the Z-axis? <br>
<br>This came a bit longish,<br>Thanks in advance,<br><br>-Shay<br><br>P.S.<br>Using Gromacs 4.0.7<br><br><br><br></div>