But be aware that the force depends on the pulling velocity. If you
perform the simulation with two different pulling velocities you'll get
two different forces for each distance.
The easiest way to get the force as a function of the distance (without
the bias of the pulling velocity) would be thermodynamik intergration.
This is similar to the umbrella sampling. You set up some windows with
different distances. But instead of restraining the distance with an
umbrella potential (as in umbrella sampling) you use a constraint to fix
the distance and than can determine the constraint force.
Greetings
Thomas
Am 17.11.2012 16:44, schrieb gmx-users-requ...@gromacs.org:
Hi Erik and Justin
Thanks, writing such a script is easy.
The point of it all would be to be able to map the magnitude of the pulling
force to what I see happen in the pulling simulation. How else would you
get an understanding of what the pulling force means?
Thanks
/PK
>
> >The only solution is to write a simple script that parses out the
>columns you want.
> >
> >-Justin
>
>I don't see the point though. Except for checking implementation of the
>pull code.
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