<div class="gmail_extra"><br><br><div class="gmail_quote">On Fri, Apr 27, 2012 at 2:53 PM, Thomas Schlesier <span dir="ltr"><<a href="mailto:schlesi@uni-mainz.de" target="_blank">schlesi@uni-mainz.de</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Am <a href="tel:27.04.2012%2015" value="+12704201215" target="_blank">27.04.2012 15</a>:31, schrieb <a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi Gmx Users,<br>
<br>
I run umbrella sampling simulation and for one window I lost my files:<br>
pullf.xvg and pullx.xvg.<br>
Is there any way to extract it based on the trajectory from this window?<br>
<br>
Steven<br>
</blockquote>
<br>
Should be possible, but you will be limited to the output-rate of your trajectory:<br></blockquote><div><br>Thank you a lot :) This sentence gave me the answer :)<br> </div><blockquote class="gmail_quote" style="margin:0pt 0pt 0pt 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
You should be able to extract the position of the pulled (PULL) and reference (REF) group from the trajectory. From this you can recalculate the pullx.xvg (think it's position of REF, then vector connecting both groups).<br>
>From the position of REF and the input for the pulling, you can calculate the position of the origin of the umbrella potential. Then just calculate the distance of the PULL to this origin to get the 'extension' -> multiply by the force constant and you get the force.<br>
<br>
If you had 'pull_geometry=distance' it's trivial:<br>
(1) 'pull_init' is distance REF to origin<br>
(2) 'g_dist' to get distance from REF to PULL<br>
(1)-(2) gives distance of PULL to origin<br>
* force constant -> force<br>
<br>
For the other options it's also straight forward:<br>
in the end you want to know the distance of the umbrella origin - PULL<br>
* from input you know the distance REF - origin<br>
* 'g_dist' gives you the distance REF - PULL<br>
<br>
Thing to note:<br>
* Depending on the using of 'pull_start' you need to modify 'pull_init'<br>
If you have 'pull_start=yes', just use 'g_dist' to get the initial distance of REF to PULL, add this to 'pull_init'<br>
* If you pull only in one dimension, just only use this dimension and not just the whole vector<br>
<br>
Greetings<span class="HOEnZb"><font color="#888888"><br>
Thomas<br>
-- <br>
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