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<div>From running a bunch of these your pullf.xvg should look like a curve and taper off at the end (go down) or you didnt reach the maximum...with the force I had to play around and started with published work for similar proteins, but had to increase the force from 1000 (published) to 2000, so a large pull force (say 2500) and then looking at the pullf.xvg gives you the max peak, which you just set it slightly over this, mine was higher than published as the protein had more affinity, if you set it too low it just acts like a horminic oscillator...with the rate, I found if there is no force, only rate, it doesn't do anything pulling apart something with a high affinity, with a small molecule the pull rate worked (I only tried this a couple times)...somone may have better suggestions,</div>
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<div>Stephan Watkins</div>
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<div style="margin:0 0 10px 0;"><b>Gesendet:</b> Dienstag, 09. Juli 2013 um 18:56 Uhr<br/>
<b>Von:</b> rookie417 <lsurampu@tulane.edu><br/>
<b>An:</b> gmx-users@gromacs.org<br/>
<b>Betreff:</b> [gmx-users] Umbrella sampling- force vs time plots</div>
<div name="quoted-content">Hello all,<br/>
<br/>
I am trying to understand the force vs time plots using Gromacs' umbrella<br/>
sampling method. I am trying to pull a short polymer chain from the interior<br/>
of a micelle and see what the PMF looks like. I use the following parameters<br/>
to run the pulling simulation for 500ps to pull the polymer over a distance<br/>
of 5nm:<br/>
<br/>
pull=umbrella<br/>
pull_geometry=direction<br/>
pull_vec1=1 0 0<br/>
pull_start=yes<br/>
pull_ngroups=1<br/>
pull_group0=surf<br/>
pull_group1=poly<br/>
pull_rate1=0.01<br/>
pull_k1=1000<br/>
<br/>
After the simulation, pullf.xvg plot I obtained is a linearly increasing<br/>
plot with time and similar result when pull_rate1=0.001 nm per ps. I am not<br/>
sure if this is right. My question is, on what basis do we select the<br/>
optimum pull_rate1 and pull_k1 for a particular system? Or is it just a<br/>
choice of parameters as long as the system does not deform? How does an<br/>
ideal force-time plot look like and does the choice of pull_k1 affect the<br/>
histogram? It appears, the entire procedure depends on the choice of input<br/>
of these two variables. I would greatly appreciate if someone can explain<br/>
this concept.<br/>
<br/>
Thanks a lot.<br/>
Andy<br/>
<br/>
<br/>
<br/>
<br/>
--<br/>
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