Sounds like this is not specific to transition path sampling.
Generally, save the trajectory and run g_dist after mdrun.
If you want to have the distance stored very often, then you should
technically be able to add the pull code with a force constant of zero
and have the pullx.xvg file track the displacement for you. Be careful
though, I have previously run into problems while trying to get too
fancy and using things in ways that the either the original developer
didn't consider or whose consequences I didn't entirely comprehend.
Here, you'll want to test that having a force constant of zero is not
going to cause some problem by running a small box of water with such
a pull-code restraint on two water molecules and checking that all
observables are the same as a control simulation that doesn't use the
pull code at all.
Chris.
-- original message --
Dear sir,
i have been doing something like transition path sampling.i
have the order parameter and i have to monitor the distance between the
ions how do i monitor the distace between the ions during the course of
simulation.should i include the order parameters in the mdp file.
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