[gmx-users] Extract pullF from trajectory

Steven Neumann s.neumann08 at gmail.com
Fri Apr 27 16:15:35 CEST 2012

On Fri, Apr 27, 2012 at 2:53 PM, Thomas Schlesier <schlesi at uni-mainz.de>wrote:

> Am 27.04.2012 15:31, schrieb gmx-users-request at gromacs.org:
>> Hi Gmx Users,
>> I run umbrella sampling simulation and for one window I lost my files:
>> pullf.xvg and pullx.xvg.
>> Is there any way to extract it based on the trajectory from this window?
>> Steven
> Should be possible, but you will be limited to the output-rate of your
> trajectory:

Thank you a lot :) This sentence gave me the answer :)

> 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).
> 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.
> If you had 'pull_geometry=distance' it's trivial:
> (1) 'pull_init' is distance REF to origin
> (2) 'g_dist' to get distance from REF to PULL
> (1)-(2) gives distance of PULL to origin
> * force constant -> force
> For the other options it's also straight forward:
> in the end you want to know the distance of the umbrella origin - PULL
> * from input you know the distance REF - origin
> * 'g_dist' gives you the distance REF - PULL
> Thing to note:
> * Depending on the using of 'pull_start' you need to modify 'pull_init'
> If you have 'pull_start=yes', just use 'g_dist' to get the initial
> distance of REF to PULL, add this to 'pull_init'
> * If you pull only in one dimension, just only use this dimension and not
> just the whole vector
> Greetings
> Thomas
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