[gmx-users] Umbrella sampling's equilibration runs

James Starlight jmsstarlight at gmail.com
Tue Apr 30 16:58:10 CEST 2013

Dear Gromacs users!

I have a question about umbrella sampling simulation based on the Justin's

According to the tutorial after definition of the set of conformers
extracted from the pulled trajectory I should run N equilibrating
simulations and N productions runs. In the tutorial I've found that all
equilibrations run in the NPT ensemble. In my case I have membrane receptor
for each conformer extracted from the pulling trajectory I want to run 20
umbrella's simulations with different starting velocities in each case.
Should I re-equilibrate each conformer in the nvt+npt runs (re-assigning
velocities in the nvt run) or the velocities might be re-assigned in the
npt equilibrations ? What the time-prolongation of each equilibrations
should be for each conformer in case of membrane protein simulation?

Thanks for help


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