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<p id="">Hi,</p>
<p> </p>
<p>I was wondering if you would be able to clear up a slightly confusing aspect of the simulations I've been running.
</p>
<p> </p>
<p>I am currently performing a pull simulation and when viewing the outputs of all the simulations I have run I see the extension of the protein stop when it reaches the same sub-domain each time (at around a 10 nm extension). The mdp file I use as the input
file states that the pull distance should be much larger than this.</p>
<p> </p>
<p>Also when viewing the -px -pf outputs this agrees. When the simulation reaches a 10 nm extension it stops and only increases around 0.2 nm over the remaining simulation time (~3000 ps). When force extension is plotted there is still an increase in force
which results in a spike at the 10 nm extension point, increasing the force from around 0.7 nN to around 30 nN.
</p>
<p> </p>
<p>Is there any reason this could be an artefact or is it just the fact that this domain is very firmly in contact with it's adjacent domain?</p>
<p> </p>
<p>Thank you for your help with this matter.</p>
<p> </p>
<p>Kind regards,</p>
<p>Natalie</p>
<p id=""> </p>
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<span style="FONT-WEIGHT: bold">Natalie Stephenson, B.Sc</span><br style="FONT-WEIGHT: bold">
<span style="FONT-WEIGHT: bold">PhD Research Associate</span><br>
<br>
Manchester Interdisciplinary Biocentre<br>
131 Princess Street<br>
Manchester<br>
M1 7DN<br>
x65816<br>
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