[gmx-users] Extract pullF from trajectory

Thomas Schlesier schlesi at uni-mainz.de
Fri Apr 27 15:53:24 CEST 2012

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 
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 
 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


More information about the gromacs.org_gmx-users mailing list