[gmx-users] regrding sampling in transtion path sampling

chris.neale at utoronto.ca chris.neale at utoronto.ca
Sun Oct 24 19:42:10 CEST 2010

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.


-- 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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