[gmx-users] Force vs distance plot in pulling simulation?
schlesi at uni-mainz.de
Sun Nov 18 14:34:36 CET 2012
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.
Am 17.11.2012 16:44, schrieb gmx-users-request at 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?
>>> > >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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