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<div>it more accuratly represents reality (my opinion), but is not feasable with high energy affinities such as protein-protein or DNA-protein interactions with short (under u or m seconds) and is used as such (I assume) in many things, or you cant pull them apart. A comparison however, would probably not show much difference ( a basketball with a small marble or even beebee thrown at it depending on what your looking at). I would say any published things should just maintain consistence, but trying one or two differences to see is research.</div>
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<div>Stephan Watkins</div>
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<div style="margin:0 0 10px 0;"><b>Gesendet:</b> Donnerstag, 08. August 2013 um 21:57 Uhr<br/>
<b>Von:</b> rookie417 <surampudi3@gmail.com><br/>
<b>An:</b> gmx-users@gromacs.org<br/>
<b>Betreff:</b> [gmx-users] Umbrella sampling - position restraints</div>
<div name="quoted-content">Dear GROMACS users,<br/>
<br/>
I followed the Umbrella Sampling tutorial to run a simple simulation of<br/>
pulling polymer chain from the surface of micelle. I used position<br/>
restraints for the initial equilibration, however I realized a typo in the<br/>
define=-DPOSRES mdp files for pulling, US_NPT and US_MD simulations later<br/>
during analysis. The simulations ran normally and the PMF plots look<br/>
accurate. However, I realized that position restraints were not applied only<br/>
after looking at the log files and position restraints energy values were<br/>
missing. The umbrella sampling MD simulation was for 2 ns only and I checked<br/>
the pullx-umbrella.xvg files and the COM fluctuations are not that bad<br/>
considering its only a short time for convergence.<br/>
<br/>
Can anyone comment on how not using position restraints would effect the<br/>
result otherwise?<br/>
<br/>
Thanks<br/>
<br/>
<br/>
<br/>
--<br/>
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